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Prokop JW, Alberta S, Witteveen-Lane M, Pell S, Farag HA, Bhargava D, Vaughan RM, Frisch A, Bauss J, Bhatti H, Arora S, Subrahmanya C, Pearson D, Goodyke A, Westgate M, Cook TW, Mitchell JT, Zieba J, Sims MD, Underwood A, Hassouna H, Rajasekaran S, Tamae Kakazu MA, Chesla D, Olivero R, Caulfield AJ. SARS-CoV-2 Genotyping Highlights the Challenges in Spike Protein Drift Independent of Other Essential Proteins. Microorganisms 2024; 12:1863. [PMID: 39338537 PMCID: PMC11433680 DOI: 10.3390/microorganisms12091863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 08/22/2024] [Accepted: 08/27/2024] [Indexed: 09/30/2024] Open
Abstract
As of 2024, SARS-CoV-2 continues to propagate and drift as an endemic virus, impacting healthcare for years. The largest sequencing initiative for any species was initiated to combat the virus, tracking changes over time at a full virus base-pair resolution. The SARS-CoV-2 sequencing represents a unique opportunity to understand selective pressures and viral evolution but requires cross-disciplinary approaches from epidemiology to functional protein biology. Within this work, we integrate a two-year genotyping window with structural biology to explore the selective pressures of SARS-CoV-2 on protein insights. Although genotype and the Spike (Surface Glycoprotein) protein continue to drift, most SARS-CoV-2 proteins have had few amino acid alterations. Within Spike, the high drift rate of amino acids involved in antibody evasion also corresponds to changes within the ACE2 binding pocket that have undergone multiple changes that maintain functional binding. The genotyping suggests selective pressure for receptor specificity that could also confer changes in viral risk. Mapping of amino acid changes to the structures of the SARS-CoV-2 co-transcriptional complex (nsp7-nsp14), nsp3 (papain-like protease), and nsp5 (cysteine protease) proteins suggest they remain critical factors for drug development that will be sustainable, unlike those strategies targeting Spike.
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Affiliation(s)
- Jeremy W. Prokop
- Office of Research, Corewell Health, Grand Rapids, MI 49503, USA; (M.W.-L.); (H.A.F.); (S.A.); (C.S.); (D.P.); (A.G.); (M.W.); (S.R.); (D.C.)
- College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; (D.B.); (R.M.V.); (A.F.); (J.B.); (H.B.); (T.W.C.); (J.T.M.); (M.A.T.K.); (R.O.)
| | - Sheryl Alberta
- Advanced Technology Lab, Corewell Health, Grand Rapids, MI 49503, USA; (S.A.); (S.P.)
| | - Martin Witteveen-Lane
- Office of Research, Corewell Health, Grand Rapids, MI 49503, USA; (M.W.-L.); (H.A.F.); (S.A.); (C.S.); (D.P.); (A.G.); (M.W.); (S.R.); (D.C.)
| | - Samantha Pell
- Advanced Technology Lab, Corewell Health, Grand Rapids, MI 49503, USA; (S.A.); (S.P.)
| | - Hosam A. Farag
- Office of Research, Corewell Health, Grand Rapids, MI 49503, USA; (M.W.-L.); (H.A.F.); (S.A.); (C.S.); (D.P.); (A.G.); (M.W.); (S.R.); (D.C.)
| | - Disha Bhargava
- College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; (D.B.); (R.M.V.); (A.F.); (J.B.); (H.B.); (T.W.C.); (J.T.M.); (M.A.T.K.); (R.O.)
| | - Robert M. Vaughan
- College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; (D.B.); (R.M.V.); (A.F.); (J.B.); (H.B.); (T.W.C.); (J.T.M.); (M.A.T.K.); (R.O.)
| | - Austin Frisch
- College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; (D.B.); (R.M.V.); (A.F.); (J.B.); (H.B.); (T.W.C.); (J.T.M.); (M.A.T.K.); (R.O.)
| | - Jacob Bauss
- College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; (D.B.); (R.M.V.); (A.F.); (J.B.); (H.B.); (T.W.C.); (J.T.M.); (M.A.T.K.); (R.O.)
| | - Humza Bhatti
- College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; (D.B.); (R.M.V.); (A.F.); (J.B.); (H.B.); (T.W.C.); (J.T.M.); (M.A.T.K.); (R.O.)
| | - Sanjana Arora
- Office of Research, Corewell Health, Grand Rapids, MI 49503, USA; (M.W.-L.); (H.A.F.); (S.A.); (C.S.); (D.P.); (A.G.); (M.W.); (S.R.); (D.C.)
| | - Charitha Subrahmanya
- Office of Research, Corewell Health, Grand Rapids, MI 49503, USA; (M.W.-L.); (H.A.F.); (S.A.); (C.S.); (D.P.); (A.G.); (M.W.); (S.R.); (D.C.)
| | - David Pearson
- Office of Research, Corewell Health, Grand Rapids, MI 49503, USA; (M.W.-L.); (H.A.F.); (S.A.); (C.S.); (D.P.); (A.G.); (M.W.); (S.R.); (D.C.)
| | - Austin Goodyke
- Office of Research, Corewell Health, Grand Rapids, MI 49503, USA; (M.W.-L.); (H.A.F.); (S.A.); (C.S.); (D.P.); (A.G.); (M.W.); (S.R.); (D.C.)
| | - Mason Westgate
- Office of Research, Corewell Health, Grand Rapids, MI 49503, USA; (M.W.-L.); (H.A.F.); (S.A.); (C.S.); (D.P.); (A.G.); (M.W.); (S.R.); (D.C.)
| | - Taylor W. Cook
- College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; (D.B.); (R.M.V.); (A.F.); (J.B.); (H.B.); (T.W.C.); (J.T.M.); (M.A.T.K.); (R.O.)
| | - Jackson T. Mitchell
- College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; (D.B.); (R.M.V.); (A.F.); (J.B.); (H.B.); (T.W.C.); (J.T.M.); (M.A.T.K.); (R.O.)
| | - Jacob Zieba
- Genetics and Genome Sciences Program, BioMolecular Science, Michigan State University, East Lansing, MI 48824, USA;
| | - Matthew D. Sims
- Section of Infectious Diseases, Corewell Health, Royal Oak, MI 48073, USA;
- Department of Internal Medicine, Oakland University William Beaumont School of Medicine, Auburn Hills, MI 48309, USA
| | - Adam Underwood
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA;
| | - Habiba Hassouna
- Adult Infectious Disease, Corewell Health, Grand Rapids, MI 49503, USA;
| | - Surender Rajasekaran
- Office of Research, Corewell Health, Grand Rapids, MI 49503, USA; (M.W.-L.); (H.A.F.); (S.A.); (C.S.); (D.P.); (A.G.); (M.W.); (S.R.); (D.C.)
- College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; (D.B.); (R.M.V.); (A.F.); (J.B.); (H.B.); (T.W.C.); (J.T.M.); (M.A.T.K.); (R.O.)
| | - Maximiliano A. Tamae Kakazu
- College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; (D.B.); (R.M.V.); (A.F.); (J.B.); (H.B.); (T.W.C.); (J.T.M.); (M.A.T.K.); (R.O.)
- Division of Pulmonary and Critical Care Medicine, Corewell Health, Grand Rapids, MI 49503, USA
| | - Dave Chesla
- Office of Research, Corewell Health, Grand Rapids, MI 49503, USA; (M.W.-L.); (H.A.F.); (S.A.); (C.S.); (D.P.); (A.G.); (M.W.); (S.R.); (D.C.)
- College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; (D.B.); (R.M.V.); (A.F.); (J.B.); (H.B.); (T.W.C.); (J.T.M.); (M.A.T.K.); (R.O.)
| | - Rosemary Olivero
- College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA; (D.B.); (R.M.V.); (A.F.); (J.B.); (H.B.); (T.W.C.); (J.T.M.); (M.A.T.K.); (R.O.)
- Pediatric Infectious Disease, Helen DeVos Children’s Hospital, Corewell Health, Grand Rapids, MI 49503, USA
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Das S, Medhi D, Talukdar AJ, Raja D, Sarma K, Sarma A, Saikia L. Hepatitis C virus genotypes among population with reported risk factors in Assam, north-east India: Emergence of genotype-8. Indian J Med Res 2024; 160:43-50. [PMID: 39382494 PMCID: PMC11463879 DOI: 10.25259/ijmr_1222_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Indexed: 10/10/2024] Open
Abstract
Background & objectives Hepatitis C virus (HCV) exhibits extensive genetic diversity in infected hosts. There are few published reports of HCV genotype (GT) distribution from the north-east Indian States lying close to the 'Golden Triangle' known for illicit drug trafficking. Real-time knowledge of HCVGT distribution is important for studies on epidemiologic aspects and virus evolution and for the development of new target-specific, direct-acting antiviral drugs. This study aims to examine the distribution of HCVGTs and their subtypes in different risk groups from Assam, north-east India. Methods It is a hospital-based cross-sectional study. Plasma samples reactive for anti-HCV antibody in enzyme-linked immunosorbent assay (ELISA) were subjected to viral load test and genotyping by real-time Reverse Transcription-Polymerase Chain Reaction (RT-PCR) or characterization of non-structural protein NS5B region by nested PCR. Nucleotide sequences were subjected to phylogenetic analysis. Results The most common HCVGT detected was GT-3 (95.89%), followed by GT-1 (3.42%), GT-6xa (0.34%) and GT-8 (0.34%). The mean age of subjects was 30.24 yr, and males outnumbered females. The most commonly associated risk factor was injecting drug use (IDU) (74.31%), followed by tattooing and/or piercing (33.22%), transfusion of blood/blood products (10.27%), and haemodialysis (9.25%). Co-infection with human immunodeficiency virus (HIV) was found in 17.8 per cent, and with Hepatitis B virus (HBV) in 3.42 per cent of the cases. Interpretation & conclusions The detection of HCVGT-8 makes this the first report from Assam and the second from India as per the authors' knowledge. This may indicate strain's endemic nature in India. The increasing trend of HCV infection among young IDUs and HCV-HIV co-infection indicates the need for enhancing surveillance and intensified prevention efforts among young adults.
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Affiliation(s)
- Sagarika Das
- Department of Microbiology, Gauhati Medical College and Hospital, Guwahati, India
| | - Devyashree Medhi
- Department of Microbiology, Dhubri Medical College and Hospital, Dhubri, India
| | | | - Dina Raja
- Department of Microbiology, Gauhati Medical College and Hospital, Guwahati, India
| | - Kishore Sarma
- Department of Computational Biology & Biotechnology, Mahapurusha Srimanta Sankaradeva Vishwavidyalaya, Nagaon, Assam, India
| | - Anisha Sarma
- Department of Microbiology, Gauhati Medical College and Hospital, Guwahati, India
| | - Lahari Saikia
- Department of Microbiology, Gauhati Medical College and Hospital, Guwahati, India
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Chen JT, Chen KJ, Wu KW, Yi SH, Shao JW. Identification and epidemiology of a novel Hepacivirus in domestic ducks in Hunan province, China. Front Vet Sci 2024; 11:1389264. [PMID: 38756518 PMCID: PMC11096584 DOI: 10.3389/fvets.2024.1389264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 04/10/2024] [Indexed: 05/18/2024] Open
Abstract
The genus Hepacivirus comprises a diverse range of genetically distinct viruses that infect both mammalian and non-mammalian hosts, with some posing significant risks to human and animal health. Members of the genus Hepacivirus are typically classified into fourteen species (Hepacivirus A-N), with ongoing discoveries of novel hepaciviruses like Hepacivirus P and Hepacivirus Q. In this study, a novel Hepacivirus was identified in duck liver samples collected from live poultry markets in Hunan province, China, using unbiased high-throughput sequencing and meta-transcriptomic analysis. Through sequence comparison and phylogenetic analysis, it was determined that this newly discovered Hepacivirus belongs to a new subspecies of Hepacivirus Q. Moreover, molecular screening revealed the widespread circulation of this novel virus among duck populations in various regions of Hunan province, with an overall prevalence of 13.3%. These findings significantly enhence our understanding of the genetic diversity and evolution of hepaciviruses, emphasizing the presence of genetically diverse hepaciviruses duck populations in China. Given the broad geographical distribution and relatively high positive rate, further investigations are essential to explore any potential associations between Hepacivirus Q and duck-related diseases.
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Affiliation(s)
- Jin-Tao Chen
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Kang-Jing Chen
- School of Medical Technology, Shangqiu Medical College, Shangqiu, China
| | - Kang-Wei Wu
- Department of Microbial Testing, Hengyang Center for Disease Control & Prevention, Hengyang, China
| | - Shan-Hong Yi
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Jian-Wei Shao
- School of Life Science and Engineering, Foshan University, Foshan, China
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Mallya S, Pissurlenkar RRS. In-silico Investigations for the Identification of Novel Inhibitors Targeting Hepatitis C Virus RNA-dependent RNA Polymerase. Med Chem 2024; 20:52-62. [PMID: 37815178 DOI: 10.2174/0115734064255683230919071808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/11/2023] [Accepted: 08/22/2023] [Indexed: 10/11/2023]
Abstract
BACKGROUND Hepatitis C is an inflammatory condition of the liver caused by the hepatitis C virus, exhibiting acute and chronic manifestations with severity ranging from mild to severe and lifelong illnesses leading to liver cirrhosis and cancer. According to the World Health Organization's global estimates, a population of about 58 million have chronic hepatitis C virus infection, with around 1.5 million new infections occurring every year. OBJECTIVE The present study aimed to identify novel molecules targeting the Hepatitis C viral RNA Dependent RNA polymerases, which play a crucial role in genome replication, mRNA synthesis, etc. Methods: Structure-based virtual screening of chemical libraries of small molecules was done using AutoDock/Vina. The top-ranking pose for every ligand was complexed with the protein and used for further protein-ligand interaction analysis using the Protein-ligand interaction Profiler. Molecules from virtual screening were further assessed using the pkCSM web server. The proteinligand interactions were further subjected to molecular dynamics simulation studies to establish dynamic stability. RESULTS Molecular docking-based virtual screening of the database of small molecules, followed by screening based on pharmacokinetic and toxicity parameters, yielded eight probable RNA Dependent RNA polymerase inhibitors. The docking scores for the proposed candidates ranged from - 8.04 to -9.10 kcal/mol. The potential stability of the ligands bound to the target protein was demonstrated by molecular dynamics simulation studies. CONCLUSION Data from exhaustive computational studies proposed eight molecules as potential anti-viral candidates, targeting Hepatitis C viral RNA Dependent RNA polymerases, which can be further evaluated for their biological potential.
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Affiliation(s)
- Shailaja Mallya
- Department of Pharmacology, Goa College of Pharmacy, Panaji Goa, 403001 India
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Curulli A. Functional Nanomaterials Enhancing Electrochemical Biosensors as Smart Tools for Detecting Infectious Viral Diseases. Molecules 2023; 28:molecules28093777. [PMID: 37175186 PMCID: PMC10180161 DOI: 10.3390/molecules28093777] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/18/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Electrochemical biosensors are known as analytical tools, guaranteeing rapid and on-site results in medical diagnostics, food safety, environmental protection, and life sciences research. Current research focuses on developing sensors for specific targets and addresses challenges to be solved before their commercialization. These challenges typically include the lowering of the limit of detection, the widening of the linear concentration range, the analysis of real samples in a real environment and the comparison with a standard validation method. Nowadays, functional nanomaterials are designed and applied in electrochemical biosensing to support all these challenges. This review will address the integration of functional nanomaterials in the development of electrochemical biosensors for the rapid diagnosis of viral infections, such as COVID-19, middle east respiratory syndrome (MERS), influenza, hepatitis, human immunodeficiency virus (HIV), and dengue, among others. The role and relevance of the nanomaterial, the type of biosensor, and the electrochemical technique adopted will be discussed. Finally, the critical issues in applying laboratory research to the analysis of real samples, future perspectives, and commercialization aspects of electrochemical biosensors for virus detection will be analyzed.
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Affiliation(s)
- Antonella Curulli
- Consiglio Nazionale delle Ricerche (CNR), Istituto per lo Studio dei Materiali Nanostrutturati (ISMN), 00161 Rome, Italy
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Chen S, Harris M. NS5A domain I antagonises PKR to facilitate the assembly of infectious hepatitis C virus particles. PLoS Pathog 2023; 19:e1010812. [PMID: 36795772 PMCID: PMC9977016 DOI: 10.1371/journal.ppat.1010812] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 03/01/2023] [Accepted: 02/02/2023] [Indexed: 02/17/2023] Open
Abstract
Hepatitis C virus NS5A is a multifunctional phosphoprotein comprised of three domains (DI, DII and DIII). DI and DII have been shown to function in genome replication, whereas DIII has a role in virus assembly. We previously demonstrated that DI in genotype 2a (JFH1) also plays a role in virus assembly, exemplified by the P145A mutant which blocked infectious virus production. Here we extend this analysis to identify two other conserved and surface exposed residues proximal to P145 (C142 and E191) that exhibited no defect in genome replication but impaired virus production. Further analysis revealed changes in the abundance of dsRNA, the size and distribution of lipid droplets (LD) and the co-localisation between NS5A and LDs in cells infected with these mutants, compared to wildtype. In parallel, to investigate the mechanism(s) underpinning this role of DI, we assessed the involvement of the interferon-induced double-stranded RNA-dependent protein kinase (PKR). In PKR-silenced cells, C142A and E191A exhibited levels of infectious virus production, LD size and co-localisation between NS5A and LD that were indistinguishable from wildtype. Co-immunoprecipitation and in vitro pulldown experiments confirmed that wildtype NS5A domain I (but not C142A or E191A) interacted with PKR. We further showed that the assembly phenotype of C142A and E191A was restored by ablation of interferon regulatory factor-1 (IRF1), a downstream effector of PKR. These data suggest a novel interaction between NS5A DI and PKR that functions to evade an antiviral pathway that blocks virus assembly through IRF1.
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Affiliation(s)
- Shucheng Chen
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Mark Harris
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
- * E-mail:
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Yuan S, Yao XY, Lian CY, Kong S, Shao JW, Zhang XL. Molecular detection and genetic characterization of bovine hepacivirus identified in ticks collected from cattle in Harbin, northeastern China. Front Vet Sci 2023; 10:1093898. [PMID: 36937022 PMCID: PMC10016144 DOI: 10.3389/fvets.2023.1093898] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 02/09/2023] [Indexed: 03/08/2023] Open
Abstract
Bovine hepacivirus (BovHepV) is a member of the genus Hepacivirus of the family Flaviviridae, which can cause acute or persistent infections in cattle. Currently, BovHepV strains identified in cattle populations worldwide can be classified into two genotypes with eight subtypes in genotype 1. BovHepV has been identified in a wide geographic area in China. Interestingly, the viral RNA of BovHepV has also been detected in ticks in Guangdong province, China. In this study, Rhipicephalus microplus tick samples were collected in Heilongjiang province, northeastern China, and BovHepV was screened with an overall positive rate of 10.9%. Sequence comparison and phylogenetic analysis showed that the BovHepV strains detected in this study belong to the subtype G. This is the first report about the detection of BovHepV in ticks in Heilongjiang province, China, which expands our knowledge that ticks may be a transmission vector of BovHepV.
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Affiliation(s)
- Sheng Yuan
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Xin-Yan Yao
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Chun-Yang Lian
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Sa Kong
- Beijing Biomedical Technology Center of Jofunhwa Biotechnology (Nanjing) Co., Ltd., Beijing, China
| | - Jian-Wei Shao
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Xue-Lian Zhang
- School of Life Science and Engineering, Foshan University, Foshan, China
- *Correspondence: Xue-Lian Zhang
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Dwivedi M, Dwivedi A, Mukherjee D. An Insight into Hepatitis C Virus: In Search of Promising Drug Targets. Curr Drug Targets 2023; 24:1127-1138. [PMID: 37907492 DOI: 10.2174/0113894501265769231020031857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/13/2023] [Accepted: 09/21/2023] [Indexed: 11/02/2023]
Abstract
Hepatitis C Virus (HCV) is a global health concern, chronically infecting over 70 million people worldwide. HCV is a bloodborne pathogen that primarily affects the liver, and chronic HCV infection can lead to cirrhosis, liver cancer, and liver failure over time. There is an urgent need for more effective approaches to prevent and treat HCV. This review summarizes current knowledge on the virology, transmission, diagnosis, and management of HCV infection. It also provides an in-depth analysis of HCV proteins as promising targets for antiviral drug and vaccine development. Specific HCV proteins discussed as potential drug targets include the NS5B polymerase, NS3/4A protease, entry receptors like CD81, and core proteins. The implications of HCV proteins as diagnostic and prognostic biomarkers are also explored. Current direct-acting antiviral therapies are effective but have cost, genotype specificity, and resistance limitations. This review aims to synthesize essential information on HCV biology and pathogenesis to inform future research on improved preventive, diagnostic, and therapeutic strategies against this global infectious disease threat.
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Affiliation(s)
- Manish Dwivedi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Gomtinagar Extension, Lucknow- 226028, India
| | - Aditya Dwivedi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Gomtinagar Extension, Lucknow- 226028, India
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Liu X, Wang L, Liang CH, Lu YP, Yang T, Zhang X. An enhanced methodology for predicting protein-protein interactions between human and hepatitis C virus via ensemble learning algorithms. J Biomol Struct Dyn 2022; 40:10592-10602. [PMID: 34251992 DOI: 10.1080/07391102.2021.1946429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Hepatitis C virus (HCV) is responsible for a variety of human life-threatening diseases, which include liver cirrhosis, chronic hepatitis, fibrosis and hepatocellular carcinoma (HCC) . Computational study of protein-protein interactions between human and HCV could boost the findings of antiviral drugs in HCV therapy and might optimize the treatment procedures for HCV infections. In this analysis, we constructed a prediction model for protein-protein interactions between HCV and human by incorporating the features generated by pseudo amino acid compositions, which were then carried out at two levels: categories and features. In brief, extra-tree was initially used for feature selection while SVM was then used to build the classification model. After that, the most suitable models for each category and each feature were selected by comparing with the three ensemble learning algorithms, that is, Random Forest, Adaboost, and Xgboost. According to our results, profile-based features were more suitable for building predictive models among the four categories. AUC value of the model constructed by Xgboost algorithm on independent data set could reach 92.66%. Moreover, Distance-based Residue, Physicochemical Distance Transformation and Profile-based Physicochemical Distance Transformation performed much better among the 17 features. AUC value of the Adaboost classifier constructed by Profile-based Physicochemical Distance Transformation on the independent dataset achieved 93.74%. Taken together, we proposed a better model with improved prediction capacity for protein-protein interactions between human and HCV in this study, which could provide practical reference for further experimental investigation into HCV-related diseases in future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Xin Liu
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Liang Wang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu, China.,Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Cheng-Hao Liang
- School of Life Science, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Ya-Ping Lu
- College of Computer Science and Technology, China University of Mining and Technology, Xuzhou, Jiangsu, China
| | - Ting Yang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Xiao Zhang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu, China
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Moustafa S, Kassela K, Bampali M, Dovrolis N, Kakkanas A, Beloukas A, Mavromara P, Karakasiliotis I. Hepatitis C Core Protein Induces a Genotype-Specific Susceptibility of Hepatocytes to TNF-Induced Death In Vitro and In Vivo. Viruses 2022; 14:v14112521. [PMID: 36423130 PMCID: PMC9692671 DOI: 10.3390/v14112521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 11/01/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
Hepatitis C virus (HCV) core protein is a multifunctional protein that is involved in the proliferation, inflammation, and apoptosis mechanism of hepatocytes. HCV core protein genetic variability has been implicated in various outcomes of HCV pathology and treatment. In the present study, we aimed to analyze the role of the HCV core protein in tumor necrosis factor α (TNFα)-induced death under the viewpoint of HCV genetic variability. Immortalized hepatocytes (IHH), and not the Huh 7.5 hepatoma cell line, stably expressing HCV subtype 4a and HCV subtype 4f core proteins showed that only the HCV 4a core protein could increase sensitivity to TNFα-induced death. Development of two transgenic mice expressing the two different core proteins under the liver-specific promoter of transthyretin (TTR) allowed for the in vivo assessment of the role of the core in TNFα-induced death. Using the TNFα-dependent model of lipopolysaccharide/D-galactosamine (LPS/Dgal), we were able to recapitulate the in vitro results in IHH cells in vivo. Transgenic mice expressing the HCV 4a core protein were more susceptible to the LPS/Dgal model, while mice expressing the HCV 4f core protein had the same susceptibility as their littermate controls. Transcriptome analysis in liver biopsies from these transgenic mice gave insights into HCV core molecular pathogenesis while linking HCV core protein genetic variability to differential pathology in vivo.
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Affiliation(s)
- Savvina Moustafa
- Molecular Virology Laboratory, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece
| | - Katerina Kassela
- Molecular Virology Laboratory, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Maria Bampali
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Nikolas Dovrolis
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Athanassios Kakkanas
- Molecular Virology Laboratory, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece
| | - Apostolos Beloukas
- National AIDS Reference Center of Southern Greece, Department of Public Health Policy, University of West Attica, 12243 Athens, Greece
- Molecular Microbiology & Immunology Lab, Department of Biomedical Sciences, University of West Attica, 11521 Athens, Greece
| | - Penelope Mavromara
- Molecular Virology Laboratory, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Ioannis Karakasiliotis
- Molecular Virology Laboratory, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece
- Correspondence:
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11
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Manjula S, Kalaiarasi C, Jaganathan R, Kumaradhas P. The effect of genotype variation and M423 resistance mutations to the binding of phosphonomidate-based inhibitor IDX17119 with the thumb-II domain of Hepatitis C virus RdRp: an integrated molecular dynamics and binding free energy study. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2136371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Affiliation(s)
- Saravanan Manjula
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
| | - Chinnasamy Kalaiarasi
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
| | - Ramakrishnan Jaganathan
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
| | - Poomani Kumaradhas
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
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12
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Chen B, Gao LY, Ma ZH, Chang H, Pei LJ, Zhou Q, Xing WG. The signal-to-cutoff ratios to predict HCV infection among people who inject drugs. Virusdisease 2022; 33:363-370. [PMID: 36278030 PMCID: PMC9579682 DOI: 10.1007/s13337-022-00797-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 10/03/2022] [Indexed: 11/22/2022] Open
Abstract
People who inject drugs (PWIDs) are primarily the high-risk population for HCV infection. This study aims to determine the optimal cut-off values for predicting HCV infection status based on the Signal-to-Cutoff (S/CO) ratio. In this study, a total of 719 PWIDs’ samples were collected, and performed for screening test by ELISA assay, and followed by RIBA assay and NAT assay to detect HCV antibody and HCV RNA levels, respectively. The findings revealed that the prevalence of HCV infection among PWIDs was 54.66% (393/719), and the false-positive rate of HCV antibody detection by ELISA assay among PWIDs was only 3.85% (16/416). In addition, when the optimal cut-off value for S/CO ratio was 2.0, the sensitivity and specificity of HCV antibody were 100.00% and 93.55%, respectively. And when the optimal cut-off value for S/CO ratio was 21.36, the sensitivity and specificity of HCV RNA positive were 89.90% and 72.73%, respectively. In conclusion, the status of HCV infection can be predicted based on the S/CO ratios of the ELISA assay, which can improve diagnosis and facilitate timely treatment to effectively prevent the spread of HCV infection.
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13
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Viral Agents as Potential Drivers of Diffuse Large B-Cell Lymphoma Tumorigenesis. Viruses 2022; 14:v14102105. [DOI: 10.3390/v14102105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 09/19/2022] [Indexed: 11/16/2022] Open
Abstract
Among numerous causative agents recognized as oncogenic drivers, 13% of total cancer cases occur as a result of viral infections. The intricacy and diversity of carcinogenic processes, however, raise significant concerns about the mechanistic function of viruses in cancer. All tumor-associated viruses have been shown to encode viral oncogenes with a potential for cell transformation and the development of malignancies, including diffuse large B-cell lymphoma (DLBCL). Given the difficulties in identifying single mechanistic explanations, it is necessary to combine ideas from systems biology and viral evolution to comprehend the processes driving viral cancer. The potential for more efficient and acceptable therapies lies in targeted medicines that aim at viral proteins or trigger immune responses to either avoid infection or eliminate infected or cancerous cells. In this review, we aim to describe the role of viral infections and their mechanistic approaches in DLBCL tumorigenesis. To the best of our knowledge, this is the first review summarizing the oncogenic potential of numerous viral agents in DLBCL development.
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14
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Behmard E, Abdulabbas HT, Abdalkareem Jasim S, Najafipour S, Ghasemian A, Farjadfar A, Barzegari E, Kouhpayeh A, Abdolmaleki P. Design of a novel multi-epitope vaccine candidate against hepatitis C virus using structural and nonstructural proteins: An immunoinformatics approach. PLoS One 2022; 17:e0272582. [PMID: 36040967 PMCID: PMC9426923 DOI: 10.1371/journal.pone.0272582] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 07/21/2022] [Indexed: 11/18/2022] Open
Abstract
Hepatitis C virus (HCV) infects the liver and causes chronic infection. Several mutations in the viral genome have been associated with drug resistance development. Currently, there is no approved vaccine against the HCV. The employment of computational biology is the primary and crucial step for vaccine design or antiviral therapy which can substantially reduce the duration and cost of studies. Therefore, in this study, we designed a multi-epitope vaccine using various immunoinformatics tools to elicit the efficient human immune responses against the HCV. Initially, various potential (antigenic, immunogenic, non-toxic and non-allergenic) epitope segments were extracted from viral structural and non-structural protein sequences using multiple screening methods. The selected epitopes were linked to each other properly. Then, toll-like receptors (TLRs) 3 and 4 agonists (50S ribosomal protein L7/L12 and human β-defensin 2, respectively) were added to the N-terminus of the final vaccine sequence to increase its immunogenicity. The 3D structure of the vaccine was modeled. Molecular dynamics simulations studies verified the high stability of final free vaccines and in complex with TLR3 and TLR4. These constructs were also antigenic, non-allergenic, nontoxic and immunogenic. Although the designed vaccine traits were promising as a potential candidate against the HCV infection, experimental studies and clinical trials are required to verify the protective traits and safety of the designed vaccine.
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Affiliation(s)
- Esmaeil Behmard
- School of Advanced Technologies in Medicine, Fasa University of Medical Sciences, Fasa, Iran
| | - Hussein T. Abdulabbas
- Department of Medical Laboratory Techniques, Faculty of Health and Medical Techniques, Imam Ja’afar Al-Sadiq University, Al Muthanna, Iraq
| | | | - Sohrab Najafipour
- School of Advanced Technologies in Medicine, Fasa University of Medical Sciences, Fasa, Iran
| | - Abdolmajid Ghasemian
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
- * E-mail: (PA); (AK); (AG)
| | - Akbar Farjadfar
- Department of Medical Biotechnology, Fasa University of Medical Sciences, Fasa, Iran
| | - Ebrahim Barzegari
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Amin Kouhpayeh
- Department of Pharmacology, Fasa University of Medical Sciences, Fasa, Iran
- * E-mail: (PA); (AK); (AG)
| | - Parviz Abdolmaleki
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- * E-mail: (PA); (AK); (AG)
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15
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Zhou Z, Zhang J, Zhou E, Ren C, Wang J, Wang Y. Small molecule NS5B RdRp non-nucleoside inhibitors for the treatment of HCV infection: A medicinal chemistry perspective. Eur J Med Chem 2022; 240:114595. [PMID: 35868125 DOI: 10.1016/j.ejmech.2022.114595] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 02/06/2023]
Abstract
Hepatitis C virus (HCV) infection has become a global health problem with enormous risks. Nonstructural protein 5B (NS5B) RNA-dependent RNA polymerase (RdRp) is a component of HCV, which can promote the formation of the viral RNA replication complex and is also an essential part of the replication complex itself. It plays a vital role in the synthesis of the positive and negative strands of HCV RNA. Therefore, the development of small-molecule inhibitors targeting NS5B RdRp is of great value for treating HCV infection-related diseases. Compared with NS5B RdRp nucleoside inhibitors, non-nucleoside inhibitors have more flexible structures, simpler mechanisms of action, and more predictable efficacy and safety of drugs in humans. Technological advances over the past decade have led to remarkable achievements in developing NS5B RdRp inhibitors. This review will summarize the non-nucleoside inhibitors targeting NS5B RdRp developed in the past decade and describe their structure optimization process and structure-activity relationship.
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Affiliation(s)
- Zhilan Zhou
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Jifa Zhang
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Tianfu Jincheng Laboratory, Chengdu, 610041, Sichuan, China
| | - Enda Zhou
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Changyu Ren
- Department of Pharmacy, Chengdu Fifth People's Hospital, Chengdu, Sichuan, 611130, China
| | - Jiaxing Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, 38163, Tennessee, United States
| | - Yuxi Wang
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Tianfu Jincheng Laboratory, Chengdu, 610041, Sichuan, China.
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16
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Frediansyah A, Sofyantoro F, Alhumaid S, Al Mutair A, Albayat H, Altaweil HI, Al-Afghani HM, AlRamadhan AA, AlGhazal MR, Turkistani SA, Abuzaid AA, Rabaan AA. Microbial Natural Products with Antiviral Activities, Including Anti-SARS-CoV-2: A Review. Molecules 2022; 27:4305. [PMID: 35807550 PMCID: PMC9268554 DOI: 10.3390/molecules27134305] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/25/2022] [Accepted: 06/29/2022] [Indexed: 02/06/2023] Open
Abstract
The SARS-CoV-2 virus, which caused the COVID-19 infection, was discovered two and a half years ago. It caused a global pandemic, resulting in millions of deaths and substantial damage to the worldwide economy. Currently, only a few vaccines and antiviral drugs are available to combat SARS-CoV-2. However, there has been an increase in virus-related research, including exploring new drugs and their repurposing. Since discovering penicillin, natural products, particularly those derived from microbes, have been viewed as an abundant source of lead compounds for drug discovery. These compounds treat bacterial, fungal, parasitic, and viral infections. This review incorporates evidence from the available research publications on isolated and identified natural products derived from microbes with anti-hepatitis, anti-herpes simplex, anti-HIV, anti-influenza, anti-respiratory syncytial virus, and anti-SARS-CoV-2 properties. About 131 compounds with in vitro antiviral activity and 1 compound with both in vitro and in vivo activity have been isolated from microorganisms, and the mechanism of action for some of these compounds has been described. Recent reports have shown that natural products produced by the microbes, such as aurasperone A, neochinulin A and B, and aspulvinone D, M, and R, have potent in vitro anti-SARS-CoV-2 activity, targeting the main protease (Mpro). In the near and distant future, these molecules could be used to develop antiviral drugs for treating infections and preventing the spread of disease.
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Affiliation(s)
- Andri Frediansyah
- PRTPP, National Research and Innovation Agency (BRIN), Yogyakarta 55861, Indonesia
| | - Fajar Sofyantoro
- Faculty of Biology, Gadjah Mada University, Yogyakarta 55281, Indonesia;
| | - Saad Alhumaid
- Administration of Pharmaceutical Care, Al-Ahsa Health Cluster, Ministry of Health, Al-Ahsa 31982, Saudi Arabia;
| | - Abbas Al Mutair
- Research Center, Almoosa Specialist Hospital, Al-Ahsa 36342, Saudi Arabia;
- College of Nursing, Princess Norah Bint Abdulrahman University, Riyadh 11564, Saudi Arabia
- School of Nursing, Wollongong University, Wollongong, NSW 2522, Australia
- Nursing Department, Prince Sultan Military College of Health Sciences, Dhahran 33048, Saudi Arabia
| | - Hawra Albayat
- Infectious Disease Department, King Saud Medical City, Riyadh 7790, Saudi Arabia;
| | - Hayyan I. Altaweil
- Department of Clinical Laboratory Sciences, Mohammed Al-Mana College of Health Sciences, Dammam 34222, Saudi Arabia;
| | - Hani M. Al-Afghani
- Laboratory Department, Security Forces Hospital, Makkah 24269, Saudi Arabia;
- Gene Center for Research and Training, Jeddah 2022, Saudi Arabia
| | - Abdullah A. AlRamadhan
- Laboratory and Toxicology Department, Security Forces Specialized Comprehensive Clinics, Al-Ahsa 36441, Saudi Arabia;
| | - Mariam R. AlGhazal
- Hematopathology Department, Dammam Regional Laboratory, Dammam 1854, Saudi Arabia;
| | | | - Abdulmonem A. Abuzaid
- Medical Microbiology Department, Security Forces Hospital Programme, Dammam 32314, Saudi Arabia;
| | - Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Public Health and Nutrition, Faculty of Basic and Applied Sciences, University of Haripur, Haripur 22610, Pakistan
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Wang R, Suzuki S, Guest JD, Heller B, Almeda M, Andrianov AK, Marin A, Mariuzza RA, Keck ZY, Foung SKH, Yunus AS, Pierce BG, Toth EA, Ploss A, Fuerst TR. Induction of broadly neutralizing antibodies using a secreted form of the hepatitis C virus E1E2 heterodimer as a vaccine candidate. Proc Natl Acad Sci U S A 2022; 119:e2112008119. [PMID: 35263223 PMCID: PMC8931252 DOI: 10.1073/pnas.2112008119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 01/19/2022] [Indexed: 11/26/2022] Open
Abstract
SignificanceHepatitis C virus chronically infects approximately 1% of the world's population, making an effective vaccine for hepatitis C virus a major unmet public health need. The membrane-associated E1E2 envelope glycoprotein has been used in clinical studies as a vaccine candidate. However, limited neutralization breadth and difficulty in producing large amounts of homogeneous membrane-associated E1E2 have hampered efforts to develop an E1E2-based vaccine. Our previous work described the design and biochemical validation of a native-like soluble secreted form of E1E2 (sE1E2). Here, we describe the immunogenic characterization of the sE1E2 complex. sE1E2 elicited broadly neutralizing antibodies in immunized mice, with increased neutralization breadth relative to the membrane-associated E1E2, thereby validating this platform as a promising model system for vaccine development.
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Affiliation(s)
- Ruixue Wang
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
| | - Saori Suzuki
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540
| | - Johnathan D. Guest
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
| | - Brigitte Heller
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540
| | - Maricar Almeda
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540
| | - Alexander K. Andrianov
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
| | - Alexander Marin
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
| | - Roy A. Mariuzza
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
| | - Zhen-Yong Keck
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305
| | - Steven K. H. Foung
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305
| | - Abdul S. Yunus
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
| | - Brian G. Pierce
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
| | - Eric A. Toth
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
| | - Alexander Ploss
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540
| | - Thomas R. Fuerst
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
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18
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Samadi M, Salimi V, Haghshenas MR, Miri SM, Mohebbi SR, Ghaemi A. Clinical and molecular aspects of human pegiviruses in the interaction host and infectious agent. Virol J 2022; 19:41. [PMID: 35264187 PMCID: PMC8905790 DOI: 10.1186/s12985-022-01769-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 01/16/2022] [Indexed: 12/11/2022] Open
Abstract
Background Human pegivirus 1 (HPgV-1) is a Positive-sense single-stranded RNA (+ ssRNA) virus, discovered in 1995 as a Flaviviridae member, and the closest human virus linked to HCV. In comparison to HCV, HPgV-1 seems to be lymphotropic and connected to the viral group that infects T and B lymphocytes. HPgV-1 infection is not persuasively correlated to any known human disease; nevertheless, multiple studies have reported a connection between chronic HPgV-1 infection and improved survival in HPgV-1/HIV co-infected patients with a delayed and favorable impact on HIV infection development. While the process has not been thoroughly clarified, different mechanisms for these observations have been proposed. HPgV-1 is categorized into seven genotypes and various subtypes. Infection with HPgV-1 is relatively common globally. It can be transferred parenterally, sexually, and through vertical ways, and thereby its co-infection with HIV and HCV is common. In most cases, the clearance of HPgV-1 from the body can be achieved by developing E2 antibodies after infection. Main body In this review, we thoroughly discuss the current knowledge and recent advances in understanding distinct epidemiological, molecular, and clinical aspects of HPgV-1. Conclusion Due to the unique characteristics of the HPgV-1, so advanced research on HPgV-1, particularly in light of HIV co-infection and other diseases, should be conducted to explore the essential mechanisms of HIV clearance and other viruses and thereby suggest novel strategies for viral therapy in the future.
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Affiliation(s)
- Mehdi Samadi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.,Department of Microbiology, Molecular and Cell-Biology Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Vahid Salimi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Haghshenas
- Department of Microbiology, Molecular and Cell-Biology Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Seyed Mohammad Miri
- Department of Virology, Pasteur Institute of Iran, P.O. Box: 1316943551, Tehran, Iran
| | - Seyed Reza Mohebbi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir Ghaemi
- Department of Virology, Pasteur Institute of Iran, P.O. Box: 1316943551, Tehran, Iran.
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19
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Zaki MYW, Fathi AM, Samir S, Eldafashi N, William KY, Nazmy MH, Fathy M, Gill US, Shetty S. Innate and Adaptive Immunopathogeneses in Viral Hepatitis; Crucial Determinants of Hepatocellular Carcinoma. Cancers (Basel) 2022; 14:1255. [PMID: 35267563 PMCID: PMC8909759 DOI: 10.3390/cancers14051255] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/01/2022] [Accepted: 02/04/2022] [Indexed: 02/08/2023] Open
Abstract
Viral hepatitis B (HBV) and hepatitis C (HCV) infections remain the most common risk factors for the development of hepatocellular carcinoma (HCC), and their heterogeneous distribution influences the global prevalence of this common type of liver cancer. Typical hepatitis infection elicits various immune responses within the liver microenvironment, and viral persistence induces chronic liver inflammation and carcinogenesis. HBV is directly mutagenic but can also cause low-grade liver inflammation characterized by episodes of intermittent high-grade liver inflammation, liver fibrosis, and cirrhosis, which can progress to decompensated liver disease and HCC. Equally, the absence of key innate and adaptive immune responses in chronic HCV infection dampens viral eradication and induces an exhausted and immunosuppressive liver niche that favors HCC development and progression. The objectives of this review are to (i) discuss the epidemiological pattern of HBV and HCV infections, (ii) understand the host immune response to acute and chronic viral hepatitis, and (iii) explore the link between this diseased immune environment and the development and progression of HCC in preclinical models and HCC patients.
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Affiliation(s)
- Marco Y. W. Zaki
- Department of Biochemistry, Faculty of Pharmacy, Minia University, Minia 61732, Egypt; (A.M.F.); (N.E.); (M.H.N.); (M.F.)
- National Institute for Health Research Birmingham Liver Biomedical Research Unit and Centre for Liver and Gastrointestinal Research, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
| | - Ahmed M. Fathi
- Department of Biochemistry, Faculty of Pharmacy, Minia University, Minia 61732, Egypt; (A.M.F.); (N.E.); (M.H.N.); (M.F.)
| | - Samara Samir
- Department of Biochemistry, Faculty of Pharmacy, Sohag University, Sohag 82524, Egypt;
| | - Nardeen Eldafashi
- Department of Biochemistry, Faculty of Pharmacy, Minia University, Minia 61732, Egypt; (A.M.F.); (N.E.); (M.H.N.); (M.F.)
| | - Kerolis Y. William
- Department of Internal Medicine, Faculty of Medicine, Cairo University, Cairo 12613, Egypt;
| | - Maiiada Hassan Nazmy
- Department of Biochemistry, Faculty of Pharmacy, Minia University, Minia 61732, Egypt; (A.M.F.); (N.E.); (M.H.N.); (M.F.)
| | - Moustafa Fathy
- Department of Biochemistry, Faculty of Pharmacy, Minia University, Minia 61732, Egypt; (A.M.F.); (N.E.); (M.H.N.); (M.F.)
| | - Upkar S. Gill
- Barts Liver Centre, Centre for Immunobiology, Barts & The London School of Medicine & Dentistry, QMUL, London E1 2AT, UK;
| | - Shishir Shetty
- National Institute for Health Research Birmingham Liver Biomedical Research Unit and Centre for Liver and Gastrointestinal Research, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
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20
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A Highly Divergent Hepacivirus Identified in Domestic Ducks Further Reveals the Genetic Diversity of Hepaciviruses. Viruses 2022; 14:v14020371. [PMID: 35215964 PMCID: PMC8879383 DOI: 10.3390/v14020371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/07/2022] [Accepted: 02/10/2022] [Indexed: 12/18/2022] Open
Abstract
Hepaciviruses represent a group of viruses that pose a significant threat to the health of humans and animals. During the last decade, new members of the genus Hepacivirus have been identified in various host species worldwide, indicating the widespread distribution of genetically diversified hepaciviruses among animals. By applying unbiased high-throughput sequencing, a novel hepacivirus, provisionally designated Hepacivirus Q, was discovered in duck liver samples collected in Guangdong province of China. Genetic analysis revealed that the complete polyprotein of Hepacivirus Q shares 23.9–46.6% amino acid identity with other representatives of the genus Hepacivirus. Considering the species demarcation criteria for hepaciviruses, Hepacivirus Q should be regarded as a novel hepacivirus species of the genus Hepacivirus within the family Flaviviridae. Phylogenetic analyses also indicate the large genetic distance between Hepacivirus Q and other known hepaciviruses. Molecular detection of this novel hepacivirus showed an overall prevalence of 15.9% in duck populations in partial areas of Guangdong province. These results expand knowledge about the genetic diversity and evolution of hepaciviruses and indicate that genetically divergent hepaciviruses are circulating in duck populations in China.
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21
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Yu Y, Wan Z, Wang JH, Yang X, Zhang C. Review of human pegivirus: Prevalence, transmission, pathogenesis, and clinical implication. Virulence 2022; 13:324-341. [PMID: 35132924 PMCID: PMC8837232 DOI: 10.1080/21505594.2022.2029328] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Human pegivirus (HPgV-1), previously known as GB virus C (GBV-C) or hepatitis G virus (HGV), is a single-stranded positive RNA virus belonging to the genus Pegivirus of the Flaviviridae family. It is transmitted by percutaneous injuries (PIs), contaminated blood and/or blood products, sexual contact, and vertical mother-to-child transmission. It is widely prevalent in general population, especially in high-risk groups. HPgV-1 viremia is typically cleared within the first 1–2 years of infection in most healthy individuals, but may persist for longer periods of time in immunocompromised individuals and/or those co-infected by other viruses. A large body of evidences indicate that HPgV-1 persistent infection has a beneficial clinical effect on many infectious diseases, such as acquired immunodeficiency syndrome (AIDS) and hepatitis C. The beneficial effects seem to be related to a significant reduction of immune activation, and/or the inhabitation of co-infected viruses (e.g. HIV-1). HPgV-1 has a broad cellular tropism for lymphoid and myeloid cells, and preferentially replicates in bone marrow and spleen without cytopathic effect, implying a therapeutic potential. The paper aims to summarize the natural history, prevalence and distribution characteristics, and pathogenesis of HPgV-1, and discuss its association with other human viral diseases, and potential use in therapy as a biovaccine or viral vector.
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Affiliation(s)
- Yaqi Yu
- College of Life Sciences, Henan Normal University, Xinxiang, China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Zhenzhou Wan
- Medical Laboratory of Taizhou Fourth People's Hospital, Taizhou, China
| | - Jian-Hua Wang
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xianguang Yang
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
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22
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Azad T, Janse van Rensburg HJ, Morgan J, Rezaei R, Crupi MJF, Chen R, Ghahremani M, Jamalkhah M, Forbes N, Ilkow C, Bell JC. Luciferase-Based Biosensors in the Era of the COVID-19 Pandemic. ACS NANOSCIENCE AU 2021; 1:15-37. [PMID: 37579261 PMCID: PMC8370122 DOI: 10.1021/acsnanoscienceau.1c00009] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Luciferase-based biosensors have a wide range of applications and assay formats, including their relatively recent use in the study of viruses. Split luciferase, bioluminescence resonance energy transfer, circularly permuted luciferase, cyclic luciferase, and dual luciferase systems have all been used to interrogate the structure and function of prominent viruses infecting humans, animals, and plants. The utility of these assays is demonstrated by numerous studies which have not only successfully characterized interactions between viral and host cell proteins but that have also used these systems to identify viral inhibitors. In the present COVID-19 pandemic, luciferase-based biosensors are already playing a critical role in the study of the culprit virus SARS-CoV-2 as well as in the development of serological assays and drug development via high-throughput screening. In this review paper, we provide a summary of existing luciferase-based biosensors and their applications in virology.
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Affiliation(s)
- Taha Azad
- Centre
for Innovative Cancer Research, Ottawa Hospital
Research Institute, Ottawa K1H 8L6, Canada
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | | | - Jessica Morgan
- Centre
for Innovative Cancer Research, Ottawa Hospital
Research Institute, Ottawa K1H 8L6, Canada
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Reza Rezaei
- Centre
for Innovative Cancer Research, Ottawa Hospital
Research Institute, Ottawa K1H 8L6, Canada
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Mathieu J. F. Crupi
- Centre
for Innovative Cancer Research, Ottawa Hospital
Research Institute, Ottawa K1H 8L6, Canada
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Rui Chen
- Centre
for Innovative Cancer Research, Ottawa Hospital
Research Institute, Ottawa K1H 8L6, Canada
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Mina Ghahremani
- Canada
Department of Biology, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Monire Jamalkhah
- Centre
for Innovative Cancer Research, Ottawa Hospital
Research Institute, Ottawa K1H 8L6, Canada
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Nicole Forbes
- Centre
for Communicable Diseases and Infection Control, Public Health Agency of Canada, Ottawa K2E 1B6, Canada
| | - Carolina Ilkow
- Centre
for Innovative Cancer Research, Ottawa Hospital
Research Institute, Ottawa K1H 8L6, Canada
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - John C. Bell
- Centre
for Innovative Cancer Research, Ottawa Hospital
Research Institute, Ottawa K1H 8L6, Canada
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
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23
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Abstract
RNA viruses cause many routine illnesses, such as the common cold and the flu. Recently, more deadly diseases have emerged from this family of viruses. The hepatitis C virus has had a devastating impact worldwide. Despite the cures developed in the U.S. and Europe, economically disadvantaged countries remain afflicted by HCV infection due to the high cost of these medications. More recently, COVID-19 has swept across the world, killing millions and disrupting economies and lifestyles; the virus responsible for this pandemic is a coronavirus. Our understanding of HCV and SARS CoV-2 replication is still in its infancy. Helicases play a critical role in the replication, transcription and translation of viruses. These key enzymes need extensive study not only as an essential player in the viral lifecycle, but also as targets for antiviral therapeutics. In this review, we highlight the current knowledge for RNA helicases of high importance to human health.
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Affiliation(s)
- John C Marecki
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Binyam Belachew
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Jun Gao
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Kevin D Raney
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States.
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24
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Ajjaji D, Ben M'barek K, Boson B, Omrane M, Gassama-Diagne A, Blaud M, Penin F, Diaz E, Ducos B, Cosset FL, Thiam AR. Hepatitis C virus core protein uses triacylglycerols to fold onto the endoplasmic reticulum membrane. Traffic 2021; 23:63-80. [PMID: 34729868 DOI: 10.1111/tra.12825] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/16/2021] [Accepted: 11/01/2021] [Indexed: 12/12/2022]
Abstract
Lipid droplets (LDs) are involved in viral infections, but exactly how remains unclear. Here, we study the hepatitis C virus (HCV) whose core capsid protein binds to LDs but is also involved in the assembly of virions at the endoplasmic reticulum (ER) bilayer. We found that the amphipathic helix-containing domain of core, D2, senses triglycerides (TGs) rather than LDs per se. In the absence of LDs, D2 can bind to the ER membrane but only if TG molecules are present in the bilayer. Accordingly, the pharmacological inhibition of the diacylglycerol O-acyltransferase enzymes, mediating TG synthesis in the ER, inhibits D2 association with the bilayer. We found that TG molecules enable D2 to fold into alpha helices. Sequence analysis reveals that D2 resembles the apoE lipid-binding region. Our data support that TG in LDs promotes the folding of core, which subsequently relocalizes to contiguous ER regions. During this motion, core may carry TG molecules to these regions where HCV lipoviroparticles likely assemble. Consistent with this model, the inhibition of Arf1/COPI, which decreases LD surface accessibility to proteins and ER-LD material exchange, severely impedes the assembly of virions. Altogether, our data uncover a critical function of TG in the folding of core and HCV replication and reveals, more broadly, how TG accumulation in the ER may provoke the binding of soluble amphipathic helix-containing proteins to the ER bilayer.
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Affiliation(s)
- Dalila Ajjaji
- Laboratoire de Physique de l'École Normale Supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, 24 rue Lhomond, Paris, 75005, France
| | - Kalthoum Ben M'barek
- Laboratoire de Physique de l'École Normale Supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, 24 rue Lhomond, Paris, 75005, France
| | - Bertrand Boson
- CIRI-Centre International de Recherche en Infectiologie, Univ Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, Lyon, France
| | - Mohyeddine Omrane
- Laboratoire de Physique de l'École Normale Supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, 24 rue Lhomond, Paris, 75005, France
| | - Ama Gassama-Diagne
- INSERM, Unité 1193, Villejuif, France.,Université Paris-Sud, UMR-S 1193, Villejuif, France
| | - Magali Blaud
- Université de Paris, CiTCoM, CNRS, Paris, France
| | - François Penin
- Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, UMR 5086, CNRS, Labex Ecofect, University of Lyon, Lyon, France
| | - Elise Diaz
- High Throughput qPCR Core Facility of the ENS, IBENS, PSL Research University, Paris, France
| | - Bertrand Ducos
- Laboratoire de Physique de l'École Normale Supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, 24 rue Lhomond, Paris, 75005, France.,High Throughput qPCR Core Facility of the ENS, IBENS, PSL Research University, Paris, France
| | - François-Loïc Cosset
- CIRI-Centre International de Recherche en Infectiologie, Univ Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, Lyon, France
| | - Abdou Rachid Thiam
- Laboratoire de Physique de l'École Normale Supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, 24 rue Lhomond, Paris, 75005, France
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25
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Shao JW, Guo LY, Yuan YX, Ma J, Chen JM, Liu Q. A Novel Subtype of Bovine Hepacivirus Identified in Ticks Reveals the Genetic Diversity and Evolution of Bovine Hepacivirus. Viruses 2021; 13:v13112206. [PMID: 34835012 PMCID: PMC8623979 DOI: 10.3390/v13112206] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/30/2021] [Accepted: 10/31/2021] [Indexed: 12/15/2022] Open
Abstract
Hepaciviruses represent a group of viruses that pose a significant threat to the health of humans and animals. New members of the genus Hepacivirus in the family Flaviviridae have recently been identified in a wide variety of host species worldwide. Similar to the Hepatitis C virus (HCV), bovine hepacivirus (BovHepV) is hepatotropic and causes acute or persistent infections in cattle. BovHepVs are distributed worldwide and classified into two genotypes with seven subtypes in genotype 1. In this study, three BovHepV strains were identified in the samples of ticks sucking blood on cattle in the Guangdong province of China, through unbiased high-throughput sequencing. Genetic analysis revealed the polyprotein-coding gene of these viral sequences herein shared 67.7–84.8% nt identity and 76.1–95.6% aa identity with other BovHepVs identified worldwide. As per the demarcation criteria adopted for the genotyping and subtyping of HCV, these three BovHepV strains belonged to a novel subtype within the genotype 1. Additionally, purifying selection was the dominant evolutionary pressure acting on the genomes of BovHepV, and genetic recombination was not common among BovHepVs. These results expand the knowledge about the genetic diversity and evolution of BovHepV distributed globally, and also indicate genetically divergent BovHepV strains were co-circulating in cattle populations in China.
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26
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Perez-Berna AJ, Benseny-Cases N, Rodríguez MJ, Valcarcel R, Carrascosa JL, Gastaminza P, Pereiro E. Monitoring reversion of hepatitis C virus-induced cellular alterations by direct-acting antivirals using cryo soft X-ray tomography and infrared microscopy. Acta Crystallogr D Struct Biol 2021; 77:1365-1377. [PMID: 34726165 PMCID: PMC8561738 DOI: 10.1107/s2059798321009955] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 09/24/2021] [Indexed: 01/01/2023] Open
Abstract
Hepatitis C virus (HCV) is an enveloped RNA virus. One of the hallmarks of HCV infection is a rearrangement of the host cell membranes, known as the `membranous web'. Full-field cryo soft X-ray tomography (cryo-SXT) in the water-window energy range (284-543 eV) was performed on the MISTRAL beamline to investigate, in whole unstained cells, the morphology of the membranous rearrangements induced in HCV replicon-harbouring cells in conditions close to the living physiological state. All morphological alterations could be reverted by a combination of sofosbuvir/daclatasvir, which are clinically approved antivirals (direct-acting antivirals; DAAs) for HCV infection. Correlatively combining cryo-SXT and 2D synchrotron-based infrared microscopy provides critical information on the chemical nature of specific infection-related structures, which allows specific patterns of the infection process or the DAA-mediated healing process to be distinguished.
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Affiliation(s)
- Ana J. Perez-Berna
- ALBA Synchrotron Light Source, Carrer de la Llum 2–26, 08290 Cerdanyola del Valles, Spain
| | - Nuria Benseny-Cases
- ALBA Synchrotron Light Source, Carrer de la Llum 2–26, 08290 Cerdanyola del Valles, Spain
| | - María José Rodríguez
- Centro Nacional de Biotecnología, Campus de Cantoblanco, Universidad Autónoma de Madrid, Madrid, Spain
| | - Ricardo Valcarcel
- ALBA Synchrotron Light Source, Carrer de la Llum 2–26, 08290 Cerdanyola del Valles, Spain
| | - José L. Carrascosa
- Centro Nacional de Biotecnología, Campus de Cantoblanco, Universidad Autónoma de Madrid, Madrid, Spain
| | - Pablo Gastaminza
- Centro Nacional de Biotecnología, Campus de Cantoblanco, Universidad Autónoma de Madrid, Madrid, Spain
| | - Eva Pereiro
- ALBA Synchrotron Light Source, Carrer de la Llum 2–26, 08290 Cerdanyola del Valles, Spain
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27
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Rafiq S, Majeed MI, Nawaz H, Rashid N, Yaqoob U, Batool F, Bashir S, Akbar S, Abubakar M, Ahmad S, Ali S, Kashif M, Amin I. Surface-enhanced Raman spectroscopy for analysis of PCR products of viral RNA of hepatitis C patients. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 259:119908. [PMID: 33989976 DOI: 10.1016/j.saa.2021.119908] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/22/2021] [Accepted: 05/02/2021] [Indexed: 06/12/2023]
Abstract
In the current study, for a qualitative and quantitative study of Polymerase Chain Reaction (PCR) products of viral RNA of Hepatitis C virus (HCV) infection, surface-enhanced Raman spectroscopy (SERS) methodology has been developed. SERS was used to identify the spectral features associated with the PCR products of viral RNA of Hepatitis C in various samples of HCV-infected patients with predetermined viral loads. The measurements for SERS were performed on 30 samples of PCR products, which included three PCR products of RNA of healthy individuals, six negative controls, and twenty-one HCV positive samples of varying viral loads (VLs) using Silver nanoparticles (Ag NPs) as a SERS substrates. Additionally, on SERS spectral data, the multivariate data analysis methods including Principal Component Analysis (PCA) and Partial Least Squares Regression (PLSR) were also carried out which help to illustrate the diagnostic capabilities of this method. The PLSR model is designed to predict HCV viral loads based on biochemical changes observed as SERS spectral features which can be associated directly with HCV RNA. Several SERS characteristic features are observed in the RNA of HCV which are not detected in the spectra of healthy RNA/controls. PCA is found helpful to differentiate the SERS spectral data sets of HCV RNA samples from healthy and negative controls. The PLSR model is found to be 99% accurate in predicting VLs of HCV RNA samples of unknown samples based on SERS spectral changes associated with the Hepatitis C development.
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Affiliation(s)
- Sidra Rafiq
- Department of Chemistry, University of Agriculture, Faisalabad 38040, Pakistan
| | | | - Haq Nawaz
- Department of Chemistry, University of Agriculture, Faisalabad 38040, Pakistan.
| | - Nosheen Rashid
- Department of Chemistry, University of Central Punjab, Faisalabad Campus, Pakistan
| | - Umer Yaqoob
- Department of Chemistry, University of Agriculture, Faisalabad 38040, Pakistan
| | - Fatima Batool
- Department of Chemistry, University of Agriculture, Faisalabad 38040, Pakistan
| | - Saba Bashir
- Department of Chemistry, University of Agriculture, Faisalabad 38040, Pakistan
| | - Saba Akbar
- Department of Chemistry, University of Agriculture, Faisalabad 38040, Pakistan
| | - Muhammad Abubakar
- Department of Chemistry, University of Agriculture, Faisalabad 38040, Pakistan
| | - Shamsheer Ahmad
- Department of Chemistry, University of Agriculture, Faisalabad 38040, Pakistan
| | - Saqib Ali
- Department of Chemistry, University of Agriculture, Faisalabad 38040, Pakistan
| | - Muhammad Kashif
- Department of Chemistry, University of Agriculture, Faisalabad 38040, Pakistan
| | - Imran Amin
- PCR Laboratory, PINUM Hospital, Faisalabad, Pakistan
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28
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Dobrica M, van Eerde A, Tucureanu C, Onu A, Paruch L, Caras I, Vlase E, Steen H, Haugslien S, Alonzi D, Zitzmann N, Bock R, Dubuisson J, Popescu C, Stavaru C, Liu Clarke J, Branza‐Nichita N. Hepatitis C virus E2 envelope glycoprotein produced in Nicotiana benthamiana triggers humoral response with virus-neutralizing activity in vaccinated mice. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2027-2039. [PMID: 34002936 PMCID: PMC8486241 DOI: 10.1111/pbi.13631] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 04/27/2021] [Accepted: 05/13/2021] [Indexed: 05/03/2023]
Abstract
Chronic infection with hepatitis C virus (HCV) remains a leading cause of liver-related pathologies and a global health problem, currently affecting more than 71 million people worldwide. The development of a prophylactic vaccine is much needed to complement the effective antiviral treatment available and achieve HCV eradication. Current strategies focus on increasing the immunogenicity of the HCV envelope glycoprotein E2, the major target of virus-neutralizing antibodies, by testing various expression systems or manipulating the protein conformation and the N-glycosylation pattern. Here we report the first evidence of successful production of the full-length HCV E2 glycoprotein in Nicotiana benthamiana, by using the Agrobacterium-mediated transient expression technology. Molecular and functional analysis showed that the viral protein was correctly processed in plant cells and achieved the native folding required for binding to CD81, one of the HCV receptors. N-glycan analysis of HCV-E2 produced in N. benthamiana and mammalian cells indicated host-specific trimming of mannose residues and possibly, protein trafficking. Notably, the plant-derived viral antigen triggered a significant immune response in vaccinated mice, characterized by the presence of antibodies with HCV-neutralizing activity. Together, our study demonstrates that N. benthamiana is a viable alternative to costly mammalian cell cultures for the expression of complex viral antigens and supports the use of plants as cost-effective production platforms for the development of HCV vaccines.
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Affiliation(s)
| | | | - Catalin Tucureanu
- Cantacuzino” Medico‐Military National Research InstituteBucharestRomania
| | - Adrian Onu
- Cantacuzino” Medico‐Military National Research InstituteBucharestRomania
| | - Lisa Paruch
- NIBIO ‐ Norwegian Institute of Bioeconomy ResearchÅsNorway
| | - Iuliana Caras
- Cantacuzino” Medico‐Military National Research InstituteBucharestRomania
| | - Ene Vlase
- Cantacuzino” Medico‐Military National Research InstituteBucharestRomania
| | - Hege Steen
- NIBIO ‐ Norwegian Institute of Bioeconomy ResearchÅsNorway
| | | | - Dominic Alonzi
- Oxford Glycobiology InstituteDepartment of BiochemistryUniversity of OxfordOxfordUK
| | - Nicole Zitzmann
- Oxford Glycobiology InstituteDepartment of BiochemistryUniversity of OxfordOxfordUK
| | - Ralph Bock
- Max Planck Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
| | - Jean Dubuisson
- Université LilleCNRSINSERMCHU LilleInstitut Pasteur de LilleU1019‐UMR 9017‐CIIL‐Center for Infection and Immunity of LilleLilleFrance
| | | | - Crina Stavaru
- Cantacuzino” Medico‐Military National Research InstituteBucharestRomania
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29
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Song X, Gao X, Wang Y, Raja R, Zhang Y, Yang S, Li M, Yao Z, Wei L. HCV Core Protein Induces Chemokine CCL2 and CXCL10 Expression Through NF-κB Signaling Pathway in Macrophages. Front Immunol 2021; 12:654998. [PMID: 34531848 PMCID: PMC8438213 DOI: 10.3389/fimmu.2021.654998] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 08/16/2021] [Indexed: 12/15/2022] Open
Abstract
HCV core protein is the first structural protein synthesized during hepatitis C virus (HCV) infection and replication. It is released from virus infected liver cells and mediates multiple functions to affect host cell response. The innate immune response is the first line of defense against viral infection. After HCV infection, Kupffer cells (KCs) which are liver macrophages play an important role in host innate immune response. Kupffer cells act as phagocytes and release different cytokines and chemokines to counter viral infection and regulate inflammation and fibrosis in liver. Earlier, we have demonstrated that HCV core protein interacts with gC1qR and activates MAPK, NF-κB and PI3K/AKT pathways in macrophages. In this study, we explored the effect of HCV core protein on CCL2 and CXCL10 expression in macrophages and the signaling pathways involved. Upon silencing of gC1qR, we observed a significant decrease expression of CCL2 and CXCL10 in macrophages in the presence of HCV core protein. Inhibiting NF-κB pathway, but not P38, JNK, ERK and AKT pathways greatly reduced the expression of CCL2 and CXCL10. Therefore, our results indicate that interaction of HCV core protein with gC1qR could induce CCL2 and CXCL10 secretion in macrophages via NF-κB signaling pathway. These findings may shed light on the understanding of how leukocytes migrate into the liver and exaggerate host-derived immune responses and may provide novel therapeutic targets in HCV chronic inflammation.
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Affiliation(s)
- Xiaotian Song
- Department of Immunology, Hebei Medical University, Shijiazhuang, China.,Key Laboratory of Immune Mechanism and Intervention on Serious Disease in Hebei Province, Shijiazhuang, China
| | - Xue Gao
- Department of Immunology, Hebei Medical University, Shijiazhuang, China.,Key Laboratory of Immune Mechanism and Intervention on Serious Disease in Hebei Province, Shijiazhuang, China
| | - Yadong Wang
- Department of Infectious Diseases, The Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Rameez Raja
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Yaoyu Zhang
- Department of Immunology, Hebei Medical University, Shijiazhuang, China.,Key Laboratory of Immune Mechanism and Intervention on Serious Disease in Hebei Province, Shijiazhuang, China
| | - Shulin Yang
- Department of Immunology, Hebei Medical University, Shijiazhuang, China.,Key Laboratory of Immune Mechanism and Intervention on Serious Disease in Hebei Province, Shijiazhuang, China
| | - Miao Li
- Department of Immunology, Hebei Medical University, Shijiazhuang, China.,Key Laboratory of Immune Mechanism and Intervention on Serious Disease in Hebei Province, Shijiazhuang, China
| | - Zhiyan Yao
- Department of Immunology, Hebei Medical University, Shijiazhuang, China.,Key Laboratory of Immune Mechanism and Intervention on Serious Disease in Hebei Province, Shijiazhuang, China
| | - Lin Wei
- Department of Immunology, Hebei Medical University, Shijiazhuang, China.,Key Laboratory of Immune Mechanism and Intervention on Serious Disease in Hebei Province, Shijiazhuang, China
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30
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Fiorino S, Tateo F, Biase DD, Gallo CG, Orlandi PE, Corazza I, Budriesi R, Micucci M, Visani M, Loggi E, Hong W, Pica R, Lari F, Zippi M. SARS-CoV-2: lessons from both the history of medicine and from the biological behavior of other well-known viruses. Future Microbiol 2021; 16:1105-1133. [PMID: 34468163 PMCID: PMC8412036 DOI: 10.2217/fmb-2021-0064] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 07/22/2021] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2 is the etiological agent of the current pandemic worldwide and its associated disease COVID-19. In this review, we have analyzed SARS-CoV-2 characteristics and those ones of other well-known RNA viruses viz. HIV, HCV and Influenza viruses, collecting their historical data, clinical manifestations and pathogenetic mechanisms. The aim of the work is obtaining useful insights and lessons for a better understanding of SARS-CoV-2. These pathogens present a distinct mode of transmission, as SARS-CoV-2 and Influenza viruses are airborne, whereas HIV and HCV are bloodborne. However, these viruses exhibit some potential similar clinical manifestations and pathogenetic mechanisms and their understanding may contribute to establishing preventive measures and new therapies against SARS-CoV-2.
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Affiliation(s)
- Sirio Fiorino
- Internal Medicine Unit, Budrio Hospital, Budrio (Bologna), Azienda USL, Bologna, 40054, Italy
| | - Fabio Tateo
- Institute of Geosciences & Earth Resources, CNR, c/o Department of Geosciences, Padova University, 35127, Italy
| | - Dario De Biase
- Department of Pharmacy & Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Claudio G Gallo
- Fisiolaserterapico Emiliano, Castel San Pietro Terme, Bologna, 40024, Italy
| | | | - Ivan Corazza
- Department of Experimental, Diagnostic & Specialty Medicine, University of Bologna, Bologna, 40126, Italy
| | - Roberta Budriesi
- Department of Pharmacy & Biotechnology, Alma Mater Studiorum-University of Bologna, Bologna, 40126, Italy
| | - Matteo Micucci
- Department of Pharmacy & Biotechnology, Alma Mater Studiorum-University of Bologna, Bologna, 40126, Italy
| | - Michela Visani
- Department of Pharmacy & Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Elisabetta Loggi
- Hepatology Unit, Department of Medical & Surgical Sciences, University of Bologna, Bologna, 40126, Italy
| | - Wandong Hong
- Department of Gastroenterology & Hepatology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, Zhejiang, 325035, PR China
| | - Roberta Pica
- Unit of Gastroenterology & Digestive Endoscopy, Sandro Pertini Hospital, Rome, 00157, Italy
| | - Federico Lari
- Internal Medicine Unit, Budrio Hospital, Budrio (Bologna), Azienda USL, Bologna, 40054, Italy
| | - Maddalena Zippi
- Unit of Gastroenterology & Digestive Endoscopy, Sandro Pertini Hospital, Rome, 00157, Italy
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31
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Gallardo-Flores CE, Colpitts CC. Cyclophilins and Their Roles in Hepatitis C Virus and Flavivirus Infections: Perspectives for Novel Antiviral Approaches. Pathogens 2021; 10:902. [PMID: 34358052 PMCID: PMC8308494 DOI: 10.3390/pathogens10070902] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/07/2021] [Accepted: 07/15/2021] [Indexed: 12/19/2022] Open
Abstract
Cyclophilins are cellular peptidyl-prolyl isomerases that play an important role in viral infections, with demonstrated roles in the replication of hepatitis C virus (HCV) and other viruses in the Flaviviridae family, such as dengue virus (DENV) and yellow fever virus (YFV). Here, we discuss the roles of cyclophilins in HCV infection and provide a comprehensive overview of the mechanisms underlying the requirement for cyclophilins during HCV replication. Notably, cyclophilin inhibitor therapy has been demonstrated to be effective in reducing HCV replication in chronically infected patients. While the roles of cyclophilins are relatively well-understood for HCV infection, cyclophilins are more recently emerging as host factors for flavivirus infection as well, providing potential new therapeutic avenues for these viral infections which currently lack antiviral therapies. However, further studies are required to elucidate the roles of cyclophilins in flavivirus replication. Here, we review the current knowledge of the role of cyclophilins in HCV infection to provide a conceptual framework to understand how cyclophilins may contribute to other viral infections, such as DENV and YFV. Improved understanding of the roles of cyclophilins in viral infection may open perspectives for the development of cyclophilin inhibitors as effective antiviral therapeutics for HCV and related viruses.
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Affiliation(s)
| | - Che C. Colpitts
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON K7L 3N6, Canada;
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32
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Boldeanu MV, Siloşi I, Bărbulescu AL, Sandu RE, Geormăneanu C, Pădureanu V, Popescu-Drigă MV, Poenariu IS, Siloşi CA, Ungureanu AM, Dijmărescu AL, Boldeanu L. Host immune response in chronic hepatitis C infection: involvement of cytokines and inflammasomes. ROMANIAN JOURNAL OF MORPHOLOGY AND EMBRYOLOGY 2021; 61:33-43. [PMID: 32747893 PMCID: PMC7728117 DOI: 10.47162/rjme.61.1.04] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chronic liver disease is a major health issue worldwide and chronic hepatitis C (CHC) is associated with an increased risk of cirrhosis and hepatocellular carcinoma (HCC). There is evidence that the hepatitis C virus (HCV) infection is correlated with immune senescence by way of immune activation and chronic inflammation, which lead to increased metabolic and cardiovascular risk, as well as progressive liver damage. Both the innate and adaptive immunity are firmly tied to the prognosis of an infection with HCV and its response to antiviral therapy. HCV is therefore associated with increased pro-inflammatory status, heightened production of cytokines, prolonged systemic inflammation, as well as increased morbidity and mortality, mainly due to the progression of hepatic fibrosis and HCC, but also secondary to cardiovascular diseases. Viral hepatic pathology is increasingly considered a disease that is no longer merely limited to the liver, but one with multiple metabolic consequences. Numerous in vitro studies, using experimental models of acute or chronic inflammation of the liver, has brought new information on immunopathological mechanisms resulting from viral infections and have highlighted the importance of involving complex structures, inflammasomes complex, in these mechanisms, in addition to the involvement of numerous proinflammatory cytokines. Beyond obtaining a sustained viral response and halting the aforementioned hepatic fibrosis, the current therapeutic “treat-to-target” strategies are presently focused on immune-mediated and metabolic disorders, to improve the quality of life and long-term prognosis of CHC patients.
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Affiliation(s)
- Mihail Virgil Boldeanu
- Department of Pharmacology, Department of Surgery, University of Medicine and Pharmacy of Craiova, Romania; ,
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Sevvana M, Keck Z, Foung SK, Kuhn RJ. Structural perspectives on HCV humoral immune evasion mechanisms. Curr Opin Virol 2021; 49:92-101. [PMID: 34091143 DOI: 10.1016/j.coviro.2021.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/15/2021] [Accepted: 05/17/2021] [Indexed: 12/20/2022]
Abstract
The molecular mechanisms of hepatitis C virus (HCV) persistence and pathogenesis are poorly understood. The design of an effective HCV vaccine is challenging despite a robust humoral immune response against closely related strains of HCV. This is primarily because of the huge genetic diversity of HCV and the molecular evolution of various virus escape mechanisms. These mechanisms are steered by the presence of a high mutational rate in HCV, structural plasticity of the immunodominant regions on the virion surface of diverse HCV genotypes, and constant amino acid substitutions on key structural components of HCV envelope glycoproteins. Here, we review the molecular basis of neutralizing antibody (nAb)-mediated immune response against diverse HCV variants, HCV-steered humoral immune evasion strategies and explore the essential structural elements to consider for designing a universal HCV vaccine. Structural perspectives on key escape pathways mediated by a point mutation within the epitope, allosteric modulation of the epitope by distant mutations and glycan shift on envelope glycoproteins will be highlighted (abstract graphic).
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Affiliation(s)
- Madhumati Sevvana
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47904, USA; Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, IN 47904, USA
| | - Zhenyong Keck
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Steven Kh Foung
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Richard J Kuhn
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47904, USA; Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, IN 47904, USA.
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34
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Péneau C, Zucman-Rossi J, Nault JC. Genomics of Viral Hepatitis-Associated Liver Tumors. J Clin Med 2021; 10:1827. [PMID: 33922394 PMCID: PMC8122827 DOI: 10.3390/jcm10091827] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 04/15/2021] [Accepted: 04/18/2021] [Indexed: 12/25/2022] Open
Abstract
Virus-related liver carcinogenesis is one of the main contributors of cancer-related death worldwide mainly due to the impact of chronic hepatitis B and C infections. Three mechanisms have been proposed to explain the oncogenic properties of hepatitis B virus (HBV) infection: induction of chronic inflammation and cirrhosis, expression of HBV oncogenic proteins, and insertional mutagenesis into the genome of infected hepatocytes. Hepatitis B insertional mutagenesis modifies the function of cancer driver genes and could promote chromosomal instability. In contrast, hepatitis C virus promotes hepatocellular carcinoma (HCC) occurrence mainly through cirrhosis development whereas the direct oncogenic role of the virus in human remains debated. Finally, adeno associated virus type 2 (AAV2), a defective DNA virus, has been associated with occurrence of HCC harboring insertional mutagenesis of the virus. Since these tumors developed in a non-cirrhotic context and in the absence of a known etiological factor, AAV2 appears to be the direct cause of tumor development in these patients via a mechanism of insertional mutagenesis altering similar oncogenes and tumor suppressor genes targeted by HBV. A better understanding of virus-related oncogenesis will be helpful to develop new preventive strategies and therapies directed against specific alterations observed in virus-related HCC.
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Affiliation(s)
- Camille Péneau
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, F-75006 Paris, France; (C.P.); (J.Z.-R.)
- Functional Genomics of Solid Tumors Laboratory, Équipe Labellisée Ligue Nationale Contre le Cancer, Labex OncoImmunology, F-75006 Paris, France
| | - Jessica Zucman-Rossi
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, F-75006 Paris, France; (C.P.); (J.Z.-R.)
- Functional Genomics of Solid Tumors Laboratory, Équipe Labellisée Ligue Nationale Contre le Cancer, Labex OncoImmunology, F-75006 Paris, France
- Hôpital Européen Georges Pompidou, APHP, F-75015 Paris, France
| | - Jean-Charles Nault
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, F-75006 Paris, France; (C.P.); (J.Z.-R.)
- Functional Genomics of Solid Tumors Laboratory, Équipe Labellisée Ligue Nationale Contre le Cancer, Labex OncoImmunology, F-75006 Paris, France
- Service d’hépatologie, Hôpital Avicenne, Hôpitaux Universitaires Paris-Seine-Saint-Denis, Assistance-Publique Hôpitaux de Paris, F-93000 Bobigny, France
- Unité de Formation et de Recherche Santé Médecine et Biologie Humaine, Université Paris Nord, F-93000 Bobigny, France
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Tarannum H, Chauhan B, Samadder A, Roy H, Nandi S. To Explore the Potential Targets and Current Structure-based Design Strategies Utilizing Co-crystallized Ligand to Combat HCV. Curr Drug Targets 2021; 22:590-604. [PMID: 32720601 DOI: 10.2174/1389450121999200727215020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/05/2020] [Accepted: 05/11/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Hepatitis C Virus (HCV) belongs to the Hepacivirus family. HCV has been designated as a very dreadful virus as it can attack the liver, causing inflammation and even may lead to cancer in chronic conditions. It was estimated that 71 million people around the world have chronic HCV infection. World Health Organization (WHO) reported that about 399000 people died because of chronic cirrhosis and liver cancer globally. In spite of the abundance of availability of drugs for the treatment of HCV, however, the issue of drug resistance surpasses all the possibilities of therapeutic management of HCV. Therefore, to address this issue of 'drug-resistance', various HCV targets were explored to quest the evaluation of the mechanism of the disease progression. METHODS An attempt has been made in the present study to explore the various targets of HCV involved in the mechanism(s) of the disease initiation and progression and to focus on the mode of binding of ligands, which are co-crystallized at the active cavity of different HCV targets. CONCLUSION The present study could predict some crucial features of these ligands, which possibly interacted with various amino acid residues responsible for their biological activity and molecular signaling pathway(s). Such binding mode may be considered as a template for the high throughput screening and designing of active congeneric ligands to combat HCV.
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Affiliation(s)
- Heena Tarannum
- Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur-244713, India
| | - Bhumika Chauhan
- Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur-244713, India
| | - Asmita Samadder
- Cytogenetics and Molecular Biology Lab., Department of Zoology, University of Kalyani, Kalyani, Nadia, 741235, India
| | - Harekrishna Roy
- Nirmala College of Pharmacy, Mangalagiri, Guntur, Andhra Pradesh, 522503, India
| | - Sisir Nandi
- Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur-244713, India
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36
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AlMalki WH, Shahid I, Abdalla AN, Johargy AK, Ahmed M, Hassan S. Virological surveillance, molecular phylogeny, and evolutionary dynamics of hepatitis C virus subtypes 1a and 4a isolates in patients from Saudi Arabia. Saudi J Biol Sci 2021; 28:1664-1677. [PMID: 33732052 PMCID: PMC7938134 DOI: 10.1016/j.sjbs.2020.11.089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/28/2020] [Accepted: 11/30/2020] [Indexed: 11/29/2022] Open
Abstract
Hepatitis C virus (HCV) subtypes are pre-requisite to predict endemicity, epidemiology, clinical pathogenesis, diagnosis, and treatment of chronic hepatitis C infection. HCV genotypes 4 and 1 are the most prevalent in Saudi Arabia, however; less consensus data exist on circulating HCV subtypes in infected individuals. This study was aimed to demonstrate the virological surveillance, phylogenetic analysis, and evolutionary relationship of HCV genotypes 4 and 1 subtypes in the Saudi population with the rest of the world. Fifty-five clinical specimens from different parts of the country were analyzed based on 5′ untranslated region (5′ UTR) amplification, direct sequencing, and for molecular evolutionary genetic analysis. Pair-wise comparison and multiple sequence alignment were performed to determine the nucleotide conservation, nucleotide variation, and positional mutations within the sequenced isolates. The evolutionary relationship of sequenced HCV isolates with referenced HCV strains from the rest of the world was established by computing pairwise genetic distances and generating phylogenetic trees. Twelve new sequences were submitted to GenBank, NCBI database. The results revealed that HCV subtype 4a is more prevalent preceded by 1a in the Saudi population. Molecular phylogeny predicts the descendants’ relationship of subtype 4a isolates very close to Egyptian prototype HCV strains, while 1a isolates were homogeneous and clustering to the European and North American genetic lineages. The implications of this study highlight the importance of HCV subtyping as an indispensable tool to monitor the distribution of viral strains, to determine the risk factors of infection prevalence, and to investigate clinical differences of treatment outcomes among intergenotypic and intragenotypic isolates in the treated population.
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Affiliation(s)
- Waleed H AlMalki
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm-Al-Qura University, Al-abidiyah, P.O. Box 13578, Makkah 21955, Saudi Arabia
| | - Imran Shahid
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm-Al-Qura University, Al-abidiyah, P.O. Box 13578, Makkah 21955, Saudi Arabia.,Department of Pharmacology and Toxicology, Faculty of Medicine, Umm-Al-Qura University, Al-abidiyah, P.O. Box 13578, Makkah 21955, Saudi Arabia
| | - Ashraf N Abdalla
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm-Al-Qura University, Al-abidiyah, P.O. Box 13578, Makkah 21955, Saudi Arabia
| | - Ayman K Johargy
- Medical Microbiology Department, Faculty of Medicine, Umm-Al-Qura University, Al-abidiyah, P.O. Box 13578, Makkah 21955, Saudi Arabia
| | - Muhammad Ahmed
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm-Al-Qura University, Al-abidiyah, P.O. Box 13578, Makkah 21955, Saudi Arabia
| | - Sajida Hassan
- Viral Hepatitis Program, Laboratory of Medicine, University of Washington, Seattle, WA, USA
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37
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Jirasko V, Lends A, Lakomek N, Fogeron M, Weber ME, Malär AA, Penzel S, Bartenschlager R, Meier BH, Böckmann A. Dimer Organization of Membrane‐Associated NS5A of Hepatitis C Virus as Determined by Highly Sensitive
1
H‐Detected Solid‐State NMR. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202013296] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
| | - Alons Lends
- Physical Chemistry ETH Zurich 8093 Zurich Switzerland
| | | | - Marie‐Laure Fogeron
- Molecular Microbiology and Structural Biochemistry Labex Ecofect UMR 5086 CNRS Université de Lyon 1 7 passage du Vercors 69367 Lyon France
| | | | | | | | - Ralf Bartenschlager
- Department of Infectious Diseases Molecular Virology Heidelberg University Im Neuenheimer Feld 345 69120 Heidelberg Germany
- German Centre for Infection Research (DZIF) Heidelberg partner site Heidelberg Germany
| | - Beat H. Meier
- Physical Chemistry ETH Zurich 8093 Zurich Switzerland
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry Labex Ecofect UMR 5086 CNRS Université de Lyon 1 7 passage du Vercors 69367 Lyon France
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38
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Jirasko V, Lends A, Lakomek N, Fogeron M, Weber ME, Malär AA, Penzel S, Bartenschlager R, Meier BH, Böckmann A. Dimer Organization of Membrane-Associated NS5A of Hepatitis C Virus as Determined by Highly Sensitive 1 H-Detected Solid-State NMR. Angew Chem Int Ed Engl 2021; 60:5339-5347. [PMID: 33205864 PMCID: PMC7986703 DOI: 10.1002/anie.202013296] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/17/2020] [Indexed: 12/17/2022]
Abstract
The Hepatitis C virus nonstructural protein 5A (NS5A) is a membrane-associated protein involved in multiple steps of the viral life cycle. Direct-acting antivirals (DAAs) targeting NS5A are a cornerstone of antiviral therapy, but the mode-of-action of these drugs is poorly understood. This is due to the lack of information on the membrane-bound NS5A structure. Herein, we present the structural model of an NS5A AH-linker-D1 protein reconstituted as proteoliposomes. We use highly sensitive proton-detected solid-state NMR methods suitable to study samples generated through synthetic biology approaches. Spectra analyses disclose that both the AH membrane anchor and the linker are highly flexible. Paramagnetic relaxation enhancements (PRE) reveal that the dimer organization in lipids requires a new type of NS5A self-interaction not reflected in previous crystal structures. In conclusion, we provide the first characterization of NS5A AH-linker-D1 in a lipidic environment shedding light onto the mode-of-action of clinically used NS5A inhibitors.
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Affiliation(s)
| | - Alons Lends
- Physical ChemistryETH Zurich8093ZurichSwitzerland
| | | | - Marie‐Laure Fogeron
- Molecular Microbiology and Structural BiochemistryLabex EcofectUMR 5086 CNRSUniversité de Lyon 17 passage du Vercors69367LyonFrance
| | | | | | | | - Ralf Bartenschlager
- Department of Infectious DiseasesMolecular VirologyHeidelberg UniversityIm Neuenheimer Feld 34569120HeidelbergGermany
- German Centre for Infection Research (DZIF)Heidelberg partner siteHeidelbergGermany
| | | | - Anja Böckmann
- Molecular Microbiology and Structural BiochemistryLabex EcofectUMR 5086 CNRSUniversité de Lyon 17 passage du Vercors69367LyonFrance
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39
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Ramesh D, Vijayakumar BG, Kannan T. Advances in Nucleoside and Nucleotide Analogues in Tackling Human Immunodeficiency Virus and Hepatitis Virus Infections. ChemMedChem 2021; 16:1403-1419. [PMID: 33427377 DOI: 10.1002/cmdc.202000849] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Indexed: 12/13/2022]
Abstract
Nucleoside and nucleotide analogues are structurally similar antimetabolites and are promising small-molecule chemotherapeutic agents against various infectious DNA and RNA viruses. To date, these analogues have not been documented in-depth as anti-human immunodeficiency virus (HIV) and anti-hepatitis virus agents, these are at various stages of testing ranging from pre-clinical, to those withdrawn from trials, or those that are approved as drugs. Hence, in this review, the importance of these analogues in tackling HIV and hepatitis virus infections is discussed with a focus on the viral genome and the mechanism of action of these analogues, both in a mutually exclusive manner and their role in HIV/hepatitis coinfection. This review encompasses nucleoside and nucleotide analogues from 1987 onwards, starting with the first nucleoside analogue, zidovudine, and going on to those in current clinical trials and even the drugs that have been withdrawn. This review also sheds light on the prospects of these nucleoside analogues in clinical trials as a treatment option for the COVID-19 pandemic.
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Affiliation(s)
- Deepthi Ramesh
- Department of Chemistry, Pondicherry University, Kalapet, Puducherry, 605014, India
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40
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Guest JD, Wang R, Elkholy KH, Chagas A, Chao KL, Cleveland TE, Kim YC, Keck ZY, Marin A, Yunus AS, Mariuzza RA, Andrianov AK, Toth EA, Foung SKH, Pierce BG, Fuerst TR. Design of a native-like secreted form of the hepatitis C virus E1E2 heterodimer. Proc Natl Acad Sci U S A 2021; 118:e2015149118. [PMID: 33431677 PMCID: PMC7826332 DOI: 10.1073/pnas.2015149118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Hepatitis C virus (HCV) is a major worldwide health burden, and a preventive vaccine is needed for global control or eradication of this virus. A substantial hurdle to an effective HCV vaccine is the high variability of the virus, leading to immune escape. The E1E2 glycoprotein complex contains conserved epitopes and elicits neutralizing antibody responses, making it a primary target for HCV vaccine development. However, the E1E2 transmembrane domains that are critical for native assembly make it challenging to produce this complex in a homogenous soluble form that is reflective of its state on the viral envelope. To enable rational design of an E1E2 vaccine, as well as structural characterization efforts, we have designed a soluble, secreted form of E1E2 (sE1E2). As with soluble glycoprotein designs for other viruses, it incorporates a scaffold to enforce assembly in the absence of the transmembrane domains, along with a furin cleavage site to permit native-like heterodimerization. This sE1E2 was found to assemble into a form closer to its expected size than full-length E1E2. Preservation of native structural elements was confirmed by high-affinity binding to a panel of conformationally specific monoclonal antibodies, including two neutralizing antibodies specific to native E1E2 and to its primary receptor, CD81. Finally, sE1E2 was found to elicit robust neutralizing antibodies in vivo. This designed sE1E2 can both provide insights into the determinants of native E1E2 assembly and serve as a platform for production of E1E2 for future structural and vaccine studies, enabling rational optimization of an E1E2-based antigen.
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Affiliation(s)
- Johnathan D Guest
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
| | - Ruixue Wang
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
| | - Khadija H Elkholy
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
- Molecular Biology Department, Genetic Engineering and Biotechnology Division, National Research Centre, Cairo 12622, Egypt
| | - Andrezza Chagas
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
| | - Kinlin L Chao
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
| | - Thomas E Cleveland
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD 20899
| | - Young Chang Kim
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305
| | - Zhen-Yong Keck
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305
| | - Alexander Marin
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
| | - Abdul S Yunus
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
| | - Roy A Mariuzza
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
| | - Alexander K Andrianov
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
| | - Eric A Toth
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
| | - Steven K H Foung
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305
| | - Brian G Pierce
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850;
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
| | - Thomas R Fuerst
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850;
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
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41
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Leroy H, Han M, Woottum M, Bracq L, Bouchet J, Xie M, Benichou S. Virus-Mediated Cell-Cell Fusion. Int J Mol Sci 2020; 21:E9644. [PMID: 33348900 PMCID: PMC7767094 DOI: 10.3390/ijms21249644] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 02/07/2023] Open
Abstract
Cell-cell fusion between eukaryotic cells is a general process involved in many physiological and pathological conditions, including infections by bacteria, parasites, and viruses. As obligate intracellular pathogens, viruses use intracellular machineries and pathways for efficient replication in their host target cells. Interestingly, certain viruses, and, more especially, enveloped viruses belonging to different viral families and including human pathogens, can mediate cell-cell fusion between infected cells and neighboring non-infected cells. Depending of the cellular environment and tissue organization, this virus-mediated cell-cell fusion leads to the merge of membrane and cytoplasm contents and formation of multinucleated cells, also called syncytia, that can express high amount of viral antigens in tissues and organs of infected hosts. This ability of some viruses to trigger cell-cell fusion between infected cells as virus-donor cells and surrounding non-infected target cells is mainly related to virus-encoded fusion proteins, known as viral fusogens displaying high fusogenic properties, and expressed at the cell surface of the virus-donor cells. Virus-induced cell-cell fusion is then mediated by interactions of these viral fusion proteins with surface molecules or receptors involved in virus entry and expressed on neighboring non-infected cells. Thus, the goal of this review is to give an overview of the different animal virus families, with a more special focus on human pathogens, that can trigger cell-cell fusion.
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Affiliation(s)
- Héloïse Leroy
- Institut Cochin, Inserm U1016, 75014 Paris, France; (H.L.); (M.H.); (M.W.)
- Centre National de la Recherche Scientifique CNRS, UMR8104, 75014 Paris, France
- Faculty of Health, University of Paris, 75014 Paris, France
| | - Mingyu Han
- Institut Cochin, Inserm U1016, 75014 Paris, France; (H.L.); (M.H.); (M.W.)
- Centre National de la Recherche Scientifique CNRS, UMR8104, 75014 Paris, France
- Faculty of Health, University of Paris, 75014 Paris, France
| | - Marie Woottum
- Institut Cochin, Inserm U1016, 75014 Paris, France; (H.L.); (M.H.); (M.W.)
- Centre National de la Recherche Scientifique CNRS, UMR8104, 75014 Paris, France
- Faculty of Health, University of Paris, 75014 Paris, France
| | - Lucie Bracq
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland;
| | - Jérôme Bouchet
- Laboratory Orofacial Pathologies, Imaging and Biotherapies UR2496, University of Paris, 92120 Montrouge, France;
| | - Maorong Xie
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK;
| | - Serge Benichou
- Institut Cochin, Inserm U1016, 75014 Paris, France; (H.L.); (M.H.); (M.W.)
- Centre National de la Recherche Scientifique CNRS, UMR8104, 75014 Paris, France
- Faculty of Health, University of Paris, 75014 Paris, France
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Roohizadeh A, Ghaffarinejad A, Salahandish R, Omidinia E. Label-free RNA-based electrochemical nanobiosensor for detection of Hepatitis C. CURRENT RESEARCH IN BIOTECHNOLOGY 2020. [DOI: 10.1016/j.crbiot.2020.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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Dent M, Hamorsky K, Vausselin T, Dubuisson J, Miyata Y, Morikawa Y, Matoba N. Safety and Efficacy of Avaren-Fc Lectibody Targeting HCV High-Mannose Glycans in a Human Liver Chimeric Mouse Model. Cell Mol Gastroenterol Hepatol 2020; 11:185-198. [PMID: 32861832 PMCID: PMC7451001 DOI: 10.1016/j.jcmgh.2020.08.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/21/2020] [Accepted: 08/25/2020] [Indexed: 12/22/2022]
Abstract
BACKGROUND & AIMS Infection with hepatitis C virus (HCV) remains a major cause of morbidity and mortality worldwide despite the recent advent of highly effective direct-acting antivirals. The envelope glycoproteins of HCV are heavily glycosylated with a high proportion of high-mannose glycans (HMGs), which serve as a shield against neutralizing antibodies and assist in the interaction with cell-entry receptors. However, there is no approved therapeutic targeting this potentially druggable biomarker. METHODS The anti-HCV activity of a fusion protein consisting of Avaren lectin and the fragment crystallizable (Fc) region of a human immunoglobulin G1 antibody, Avaren-Fc (AvFc) was evaluated through the use of in vitro neutralization assays as well as an in vivo challenge in a chimeric human liver (PXB) mouse model. Drug toxicity was assessed by histopathology, serum alanine aminotransferase, and mouse body weights. RESULTS AvFc was capable of neutralizing cell culture-derived HCV in a genotype-independent manner, with 50% inhibitory concentration values in the low nanomolar range. Systemic administration of AvFc in a histidine-based buffer was well tolerated; after 11 doses every other day at 25 mg/kg there were no significant changes in body or liver weights or in blood human albumin or serum alanine aminotransferase activity. Gross necropsy and liver pathology confirmed the lack of toxicity. This regimen successfully prevented genotype 1a HCV infection in all animals, although an AvFc mutant lacking HMG binding activity failed. CONCLUSIONS These results suggest that targeting envelope HMGs is a promising therapeutic approach against HCV infection, and AvFc may provide a safe and efficacious means to prevent recurrent infection upon liver transplantation in HCV-related end-stage liver disease patients.
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Affiliation(s)
| | - Krystal Hamorsky
- Department of Medicine; James Graham Brown Cancer Center; Center for Predictive Medicine, University of Louisville School of Medicine, Louisville, Kentucky
| | - Thibaut Vausselin
- University of Lille, Centre national de la recherche scientifique, INSERM, Centre Hospitalier Universitaire Lille, Institut Pasteur de Lille, U1019, UMR 8204, Center for Infection and Immunity of Lille, Lille, France
| | - Jean Dubuisson
- University of Lille, Centre national de la recherche scientifique, INSERM, Centre Hospitalier Universitaire Lille, Institut Pasteur de Lille, U1019, UMR 8204, Center for Infection and Immunity of Lille, Lille, France
| | | | | | - Nobuyuki Matoba
- Department of Pharmacology and Toxicology; James Graham Brown Cancer Center; Center for Predictive Medicine, University of Louisville School of Medicine, Louisville, Kentucky.
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Laursen TL, Sandahl TD, Kazankov K, George J, Grønbæk H. Liver-related effects of chronic hepatitis C antiviral treatment. World J Gastroenterol 2020; 26:2931-2947. [PMID: 32587440 PMCID: PMC7304101 DOI: 10.3748/wjg.v26.i22.2931] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/26/2020] [Accepted: 05/29/2020] [Indexed: 02/06/2023] Open
Abstract
More than five years ago, the treatment of hepatitis C virus infection was revolutionized with the introduction of all-oral direct-acting antiviral (DAA) drugs. They proved highly efficient in curing patients with chronic hepatitis C (CHC), including patients with cirrhosis. The new DAA treatments were alleged to induce significant improvements in clinical outcome and prognosis, but the exact cause of the expected benefit was unclear. Further, little was known about how the underlying liver disease would be affected during and after viral clearance. In this review, we describe and discuss the liver-related effects of the new treatments in regards to both pathophysiological aspects, such as macrophage activation, and the time-dependent effects of therapy, with specific emphasis on inflammation, structural liver changes, and liver function, as these factors are all related to morbidity and mortality in CHC patients. It seems clear that antiviral therapy, especially the achievement of a sustained virologic response has several beneficial effects on liver-related parameters in CHC patients with advanced liver fibrosis or cirrhosis. There seems to be a time-dependent effect of DAA therapy with viral clearance and the resolution of liver inflammation followed by more discrete changes in structural liver lesions. These improvements lead to favorable effects on liver function, followed by an improvement in cognitive dysfunction and portal hypertension. Overall, the data provide knowledge on the several beneficial effects of DAA therapy on liver-related parameters in CHC patients suggesting short- and long-term improvements in the underlying disease with the promise of an improved long-term prognosis.
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Affiliation(s)
- Tea L Laursen
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus N DK-8200, Denmark
| | - Thomas D Sandahl
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus N DK-8200, Denmark
| | - Konstantin Kazankov
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus N DK-8200, Denmark
| | - Jacob George
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital, Sydney NSW 2145, Australia
- University of Sydney, Sydney NSW 2145, Australia
| | - Henning Grønbæk
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus N DK-8200, Denmark
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B UR, Tandon H, Pradhan MK, Adhikesavan H, Srinivasan N, Das S, Jayaraman N. Potent HCV NS3 Protease Inhibition by a Water-Soluble Phyllanthin Congener. ACS OMEGA 2020; 5:11553-11562. [PMID: 32478245 PMCID: PMC7254805 DOI: 10.1021/acsomega.0c00786] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 04/30/2020] [Indexed: 05/04/2023]
Abstract
NS3/4A protease of hepatitis C virus (HCV) plays an important role in viral RNA replication. A 1,4-diphenylbutanedicarboxylic acid derivative, namely, phyllanthin, extracted from the leaf of a herbal plant, Phyllanthus amarus, inhibits HCV NS3/4A protease and replication activities. However, the reduced aqueous solubility, high toxicity, and poor oral bioavailability are major impediments with phyllanthin. We herein present a design approach to generate phyllanthin congeners in order to potentiate inhibition activity against protease. The phyllanthin congeners were synthesized by chemical methods and subjected to systematic biological studies. One of the congeners, annotated as D8, is identified as a novel and potent inhibitor of the HCV-NS3/4Aprotease activity in vitro and the viral RNA replication in cell culture. Structural analysis using the computational-based docking approach demonstrated important noncovalent interactions between D8 and the catalytic residues of the viral protease. Furthermore, D8 was found to be significantly nontoxic in cell culture. More importantly, oral administration of D8 in BALB/c mice proved its better tolerability and bioavailability, as compared to native phyllanthin. Taken together, this study reveals a promising candidate for developing anti-HCV therapeutics to control HCV-induced liver diseases.
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Affiliation(s)
- Uma Reddy B
- Microbiology and
Cell Biology, Indian Institute of Science, Bangalore 560 012, India
| | - Himani Tandon
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Manoj K. Pradhan
- Department
of Organic Chemistry, Indian Institute of
Science, Bangalore 560 012, India
| | | | | | - Saumitra Das
- Microbiology and
Cell Biology, Indian Institute of Science, Bangalore 560 012, India
- National Institute
of Biomedical Genomics, Kalyani 741 251, India
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Malik AA, Phanus-Umporn C, Schaduangrat N, Shoombuatong W, Isarankura-Na-Ayudhya C, Nantasenamat C. HCVpred: A web server for predicting the bioactivity of hepatitis C virus NS5B inhibitors. J Comput Chem 2020; 41:1820-1834. [PMID: 32449536 DOI: 10.1002/jcc.26223] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/10/2020] [Accepted: 04/28/2020] [Indexed: 02/06/2023]
Abstract
Hepatitis C virus (HCV) is one of the major causes of liver disease affecting an estimated 170 million people culminating in 300,000 deaths from cirrhosis or liver cancer. NS5B is one of three potential therapeutic targets against HCV (i.e., the other two being NS3/4A and NS5A) that is central to viral replication. In this study, we developed a classification structure-activity relationship (CSAR) model for identifying substructures giving rise to anti-HCV activities among a set of 578 non-redundant compounds. NS5B inhibitors were described by a set of 12 fingerprint descriptors and predictive models were constructed from 100 independent data splits using the random forest algorithm. The modelability (MODI index) of the data set was determined to be robust with a value of 0.88 exceeding established threshold of 0.65. The predictive performance was deduced by the accuracy, sensitivity, specificity, and Matthews correlation coefficient, which was found to be statistically robust (i.e., the former three parameters afforded values in excess of 0.8 while the latter statistical parameter provided a value >0.7). An in-depth analysis of the top 20 important descriptors revealed that aromatic ring and alkyl side chains are important for NS5B inhibition. Finally, the predictive model is deployed as a publicly accessible HCVpred web server (available at http://codes.bio/hcvpred/) that would allow users to predict the biological activity as being active or inactive against HCV NS5B. Thus, the knowledge and web server presented herein can be used in the design of more potent and specific drugs against the HCV NS5B.
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Affiliation(s)
- Aijaz Ahmad Malik
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Chuleeporn Phanus-Umporn
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Nalini Schaduangrat
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Watshara Shoombuatong
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | | | - Chanin Nantasenamat
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
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The Host Factor Erlin-1 is Required for Efficient Hepatitis C Virus Infection. Cells 2019; 8:cells8121555. [PMID: 31810281 PMCID: PMC6953030 DOI: 10.3390/cells8121555] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/28/2019] [Accepted: 11/29/2019] [Indexed: 12/22/2022] Open
Abstract
Development of hepatitis C virus (HCV) infection cell culture systems has permitted the identification of cellular factors that regulate the HCV life cycle. Some of these cellular factors affect steps in the viral life cycle that are tightly associated with intracellular membranes derived from the endoplasmic reticulum (ER). Here, we describe the discovery of erlin-1 protein as a cellular factor that regulates HCV infection. Erlin-1 is a cholesterol-binding protein located in detergent-resistant membranes within the ER. It is implicated in cholesterol homeostasis and the ER-associated degradation pathway. Silencing of erlin-1 protein expression by siRNA led to decreased infection efficiency characterized by reduction in intracellular RNA accumulation, HCV protein expression and virus production. Mechanistic studies revealed that erlin-1 protein is required early in the infection, downstream of cell entry and primary translation, specifically to initiate RNA replication, and later in the infection to support infectious virus production. This study identifies erlin-1 protein as an important cellular factor regulating HCV infection.
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Serine 229 Balances the Hepatitis C Virus Nonstructural Protein NS5A between Hypo- and Hyperphosphorylated States. J Virol 2019; 93:JVI.01028-19. [PMID: 31511391 DOI: 10.1128/jvi.01028-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/08/2019] [Indexed: 12/19/2022] Open
Abstract
The nonstructural protein NS5A of hepatitis C virus (HCV) is a phosphorylated protein that is indispensable for viral replication and assembly. We previously showed that NS5A undergoes sequential serine S232/S235/S238 phosphorylation resulting in NS5A transition from a hypo- to a hyperphosphorylated state. Here, we studied functions of S229 with a newly generated antibody specific to S229 phosphorylation. In contrast to S232, S235, or S238 phosphorylation detected only in the hyperphosphorylated NS5A, S229 phosphorylation was found in both hypo- and hyperphosphorylated NS5A, suggesting that S229 phosphorylation initiates NS5A sequential phosphorylation. Immunoblotting showed an inverse relationship between S229 phosphorylation and S235 phosphorylation. When S235 was phosphorylated as in the wild-type NS5A, the S229 phosphorylation level was low; when S235 could not be phosphorylated as in the S235A mutant NS5A, the S229 phosphorylation level was high. These results suggest an intrinsic feedback regulation between S229 phosphorylation and S235 phosphorylation. It has been known that NS5A distributes in large static and small dynamic intracellular structures and that both structures are required for the HCV life cycle. We found that S229A or S229D mutation was lethal to the virus and that both increased NS5A in large intracellular structures. Similarly, the lethal S235A mutation also increased NS5A in large structures. Likewise, the replication-compromised S235D mutation also increased NS5A in large structures, albeit to a lesser extent. Our data suggest that S229 probably cycles through phosphorylation and dephosphorylation to maintain a delicate balance of NS5A between hypo- and hyperphosphorylated states and the intracellular distribution necessary for the HCV life cycle.IMPORTANCE This study joins our previous efforts to elucidate how NS5A transits between hypo- and hyperphosphorylated states via phosphorylation on a series of highly conserved serine residues. Of the serine residues, serine 229 is the most interesting since phosphorylation-mimicking and phosphorylation-ablating mutations at this serine residue are both lethal. With a new high-quality antibody specific to serine 229 phosphorylation, we concluded that serine 229 must remain wild type so that it can dynamically cycle through phosphorylation and dephosphorylation that govern NS5A between hypo- and hyperphosphorylated states. Both are required for the HCV life cycle. When phosphorylated, serine 229 signals phosphorylation on serine 232 and 235 in a sequential manner, leading NS5A to the hyperphosphorylated state. As serine 235 phosphorylation is reached, serine 229 is dephosphorylated, stopping signal for hyperphosphorylation. This balances NS5A between two phosphorylation states and in intracellular structures that warrant a productive HCV life cycle.
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Nazario de Moraes L, Tommasini Grotto RM, Targino Valente G, de Carvalho Sampaio H, Magro AJ, Fogaça L, Wolf IR, Perahia D, Faria Silva G, Plana Simões R. A novel molecular mechanism to explain mutations of the HCV protease associated with resistance against covalently bound inhibitors. Virus Res 2019; 274:197778. [PMID: 31618615 DOI: 10.1016/j.virusres.2019.197778] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/07/2019] [Accepted: 10/08/2019] [Indexed: 02/07/2023]
Abstract
NS3 is an important therapeutic target for direct-acting antiviral (DAA) drugs. However, many patients treated with DAAs have unsustained virologic response (UVR) due to the high mutation rate of HCV. The aim of this work was to shed some light on the puzzling molecular mechanisms of the virus's of patients who showed high viral loads even under treatment with DAA. Bioinformatics tools, molecular modelling analyses were employed to identify mutations associated with HCV resistance to boceprevir and possible structural features related to this phenomenon. We identified two mutations of NS3 that may be associated with HCV resistance: D168N and L153I. The substitution D168N was previously reported in the literature as related with drug failure. Additionally, we identified that its molecular resistance mechanism can be explained by the destabilization of receptor-ligand hydrogen bonds. For the L153I mutation, the resistance mechanism is different from previous models reported in the literature. The L153I substitution decreases the S139 deprotonation susceptibility, and consequently, this mutation impairs the covalent binding between the residue S139 from NS3 and the electrophilic trap on boceprevir, which can induce drug failure. These results were supported by the time course analysis of the mutations of the NS3 protease, which showed that boceprevir was designed for enzymes with an L residue at position 153; however, the sequences with I153 are predominant nowadays. The results presented here could be used to infer about resistance in others DAA, mainly protease inhibitors.
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Affiliation(s)
- Leonardo Nazario de Moraes
- Sao Paulo State University (UNESP), School of Agriculture, Department of Bioprocess and Biotechnology, Avenue Universitária, 3780, Botucatu, SP, Brazil
| | - Rejane Maria Tommasini Grotto
- Sao Paulo State University (UNESP), School of Agriculture, Department of Bioprocess and Biotechnology, Avenue Universitária, 3780, Botucatu, SP, Brazil; Sao Paulo State University (UNESP), Medical School, Blood Center, Avenue Prof. Mário Rubens Guimarães Montenegro, s/n, Botucatu, SP, Brazil
| | - Guilherme Targino Valente
- Sao Paulo State University (UNESP), School of Agriculture, Department of Bioprocess and Biotechnology, Avenue Universitária, 3780, Botucatu, SP, Brazil; Max Planck Institut for Heart and Lung Research, Ludwigstraße 43, 61231, Bad Nauheim, Germany
| | - Heloisa de Carvalho Sampaio
- Sao Paulo State University (UNESP), Medical School, Blood Center, Avenue Prof. Mário Rubens Guimarães Montenegro, s/n, Botucatu, SP, Brazil
| | - Angelo José Magro
- Sao Paulo State University (UNESP), School of Agriculture, Department of Bioprocess and Biotechnology, Avenue Universitária, 3780, Botucatu, SP, Brazil; Sao Paulo State University (UNESP), Medical School, Blood Center, Avenue Prof. Mário Rubens Guimarães Montenegro, s/n, Botucatu, SP, Brazil; Sao Paulo State University (UNESP), Institute of Biosciences, Street Prof. Dr. Antônio Celso Wagner Zanin, 250, Botucatu, SP, Brazil
| | - Lauana Fogaça
- Sao Paulo State University (UNESP), School of Agriculture, Department of Bioprocess and Biotechnology, Avenue Universitária, 3780, Botucatu, SP, Brazil; Sao Paulo State University (UNESP), Institute of Biosciences, Street Prof. Dr. Antônio Celso Wagner Zanin, 250, Botucatu, SP, Brazil
| | - Ivan Rodrigo Wolf
- Sao Paulo State University (UNESP), Institute of Biosciences, Street Prof. Dr. Antônio Celso Wagner Zanin, 250, Botucatu, SP, Brazil
| | - David Perahia
- École Normale Supérieure Paris-Saclay, Laboratory of Biology and Applied Pharmacology, Cachan, 94235, France
| | - Giovanni Faria Silva
- Sao Paulo State University (UNESP), Medical School, Blood Center, Avenue Prof. Mário Rubens Guimarães Montenegro, s/n, Botucatu, SP, Brazil
| | - Rafael Plana Simões
- Sao Paulo State University (UNESP), School of Agriculture, Department of Bioprocess and Biotechnology, Avenue Universitária, 3780, Botucatu, SP, Brazil; Sao Paulo State University (UNESP), Medical School, Blood Center, Avenue Prof. Mário Rubens Guimarães Montenegro, s/n, Botucatu, SP, Brazil.
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Khan MA, Khan SA, Hamayun M, Ali M, Idrees M. Sequence variability of HCV 3a isolates based on core gene in patients from Lahore, Pakistan. Future Virol 2019. [DOI: 10.2217/fvl-2019-0086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Aim: To investigate the HCV 3a core sequence variation and amino acid substitutions of patients from Lahore, Pakistan. Materials & methods: Blood samples from HCV positive patients (n = 232) were collected for viral genotypes. Moreover, the nucleotide sequencing was performed for core gene of 20 samples. Results: Viral genotyping showed that 69.82% (n = 162) belonged to 3a genotype, 9.05% (1a; n = 21), 2.15% (3b; n = 5) and 18.98% were untypable (n = 44). Phylogenetic analyses suggest majority of our isolates clustered with previously reported reference isolates from Pakistan. The remaining isolates clustered with HCV-core sequences reported from Vietnam, Japan, Thailand, Iran, USA, Bangladesh, Malaysia and Morocco. Conclusion: We report HCV-core substitutions (G60E, R70Q, C91A, A94Q and Q63E/D) that could be associated with treatment response in Pakistani patients.
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Affiliation(s)
- Muhammad Ajmal Khan
- Center for Biotechnology & Microbiology (COBAM), University of Peshawar, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Sumera Afzal Khan
- Center for Biotechnology & Microbiology (COBAM), University of Peshawar, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Hamayun
- Department of Botany, Abdul Wali Khan University Mardan, Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Ali
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Idrees
- National Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
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